Birnbaum‐Saunders distribution: A review of models,analysis, and applications

Birnbaum and Saunders introduced a two‐parameter lifetime distribution to model the fatigue life of a metal, subject to cyclic stress. Since then, extensive work has been done on this model providing different interpretations, constructions, generalizations, inferential methods, and extensions to bivariate, multivariate, and matrix‐variate cases. More than 200 papers and one research monograph have already appeared describing all these aspects and developments. In this paper, we provide a detailed review of all these developments and, at the same time, indicate several open problems that could be considered for further research.     

Transmembrane Signaling with Lipid‐Bilayer Assemblies as a Platform for Channel‐Based Biosensing

Artificial and natural lipid membranes that elicit transmembrane signaling is are useful as a platform for channel‐based biosensing. In this account we summarize our research on the design of transmembrane signaling associated with lipid bilayer membranes containing nanopore‐forming compounds. Channel‐forming compounds, such as receptor ion‐channels, channel‐forming peptides and synthetic channels, are embedded in planar and spherical bilayer lipid membranes to develop highly sensitive and selective biosensing methods for a variety of analytes. The membrane‐bound receptor approach is useful for introducing receptor sites on both planar and spherical bilayer lipid membranes. Natural receptors in biomembranes are also used for designing of biosensing methods.     

Tractable Partially Ordered Sets Derived from Root Systems and Biased Graphs

We study new posets Q obtained by removing from a geometric lattice L ofa biased graph certain flats indexed by a simplicial complex . (One example of L is the lattice of flats of thevector matroid of a root system B _n .) We study the structureand compute the characteristic polynomial of Q. With certainchoices of L and , including ones for which Q is alattice interpolating between those of B _n and D _n , we observe curious relationships among the roots of thecharacteristic polynomials of Q, L, and .     

基于液相色谱-串联质谱技术的磷酸化蛋白质组学分析

本文运用稳定同位素双甲基化标记技术、固定相金属离子螯合层析(IMAC)技术并结合液相色谱-串联质谱法研究了仙台病毒感染引起的宿主细胞磷酸化蛋白质组变化。实验发现定量的4 289个磷酸化肽段有~20%的蛋白质磷酸化位点发生了显著变化;通路富集分析表明哺乳动物雷帕毒素靶蛋白(mTOR)通路和剪接体(Spliceosome)通路可能参与宿主细胞对病毒的应答;通过对显著变化磷酸化肽段进行基序分析,发现了9个代表性的磷酸化修饰位点基序。本研究方法对于深入解析抗病毒天然免疫信号通路提供了新线索。     

Dynamic conformational ensembles regulate casein kinase-1 isoforms: Insights from molecular dynamics and molecular docking studies

Casein kinase-1 (CK1) isoforms actively participate in the down-regulation of canonical Wnt signaling pathway; however recent studies have shown their active roles in oncogenesis of various tissues through this pathway. Functional loss of two isoforms (CK1-α/ε) has been shown to activate the carcinogenic pathway which involves the stabilization of of cytoplasmic β-catenin. Development of anticancer therapeutics is very laborious task and depends upon the structural and conformational details of the target. This study focuses on, how the structural dynamics and conformational changes of two CK1 isoforms are synchronized in carcinogenic pathway. The conformational dynamics in kinases is the responsible for their action as has been supported by the molecular docking experiments.     

Integrated Network Pharmacology Analysis and In Vitro Validation Revealed the Potential Active Components and Underlying Mechanistic Pathways of Herba Patriniae in Colorectal Cancer

Herba Patriniae (HP) are medicinal plants commonly used in colorectal cancer (CRC) patients. In this study, network pharmacology was used to predict the active components and key signaling pathways of HP in CRC. Patrinia heterophylla, one type of HP, was chosen for validation of the network pharmacology analysis. The phytochemical profile of Patrinia heterophylla water extract (PHW) was determined by UHPLC-MS. MTT, RT-PCR, and Western blot assays were performed to evaluate the bioactivities of PHW in colon cancer cells. Results showed that 15 potentially active components of HP interacted with 28 putative targets of CRC in the compound–target network, of which asperglaucide had the highest degree. Furthermore, the ErbB signaling pathway was identified as the pathway mediated by HP with the most potential against CRC. Both RT-PCR and Western blot results showed that PHW significantly downregulated the mRNA and protein levels of EGFR, PI3K, and AKT in HCT116 cells. Asperglaucide, present in PHW, exhibited an anti-migratory effect in HCT116 cells, suggesting that it could be an active component of PHW in CRC treatment. In conclusion, this study has provided the first scientific evidence to support the use of PHW in CRC and paved the way for further research into the underlying mechanisms of PHW against CRC.     

Domain Analysis and Motif Matcher (DAMM): A Program to Predict Selectivity Determinants in Monosiga brevicollis PDZ Domains Using Human PDZ Data

Choanoflagellates are single-celled eukaryotes with complex signaling pathways. They are considered the closest non-metazoan ancestors to mammals and other metazoans and form multicellular-like states called rosettes. The choanoflagellate Monosiga brevicollis contains over 150 PDZ domains, an important peptide-binding domain in all three domains of life (Archaea, Bacteria, and Eukarya). Therefore, an understanding of PDZ domain signaling pathways in choanoflagellates may provide insight into the origins of multicellularity. PDZ domains recognize the C-terminus of target proteins and regulate signaling and trafficking pathways, as well as cellular adhesion. Here, we developed a computational software suite, Domain Analysis and Motif Matcher (DAMM), that analyzes peptide-binding cleft sequence identity as compared with human PDZ domains and that can be used in combination with literature searches of known human PDZ-interacting sequences to predict target specificity in choanoflagellate PDZ domains. We used this program, protein biochemistry, fluorescence polarization, and structural analyses to characterize the specificity of A9UPE9_MONBE, a M. brevicollis PDZ domain-containing protein with no homology to any metazoan protein, finding that its PDZ domain is most similar to those of the DLG family. We then identified two endogenous sequences that bind A9UPE9 PDZ with <100 μM affinity, a value commonly considered the threshold for cellular PDZ–peptide interactions. Taken together, this approach can be used to predict cellular targets of previously uncharacterized PDZ domains in choanoflagellates and other organisms. Our data contribute to investigations into choanoflagellate signaling and how it informs metazoan evolution.     

P2Y12 Purinergic Receptor and Brain Tumors: Implications on Glioma Microenvironment

Gliomas are the most common malignant brain tumors in adults, characterized by a high proliferation and invasion. The tumor microenvironment is rich in growth-promoting signals and immunomodulatory pathways, which increase the tumor’s aggressiveness. In response to hypoxia and glioma therapy, the amounts of adenosine triphosphate (ATP) and adenosine diphosphate (ADP) strongly increase in the extracellular space, and the purinergic signaling is triggered by nucleotides’ interaction in P2 receptors. Several cell types are present in the tumor microenvironment and can facilitate tumor growth. In fact, tumor cells can activate platelets by the ADP-P2Y₁₂ engagement, which plays an essential role in the cancer context, protecting tumors from the immune attack and providing molecules that contribute to the growth and maintenance of a rich environment to sustain the protumor cycle. Besides platelets, the P2Y₁₂ receptor is expressed by some tumors, such as renal carcinoma, colon carcinoma, and gliomas, being related to tumor progression. In this context, this review aims to depict the glioma microenvironment, focusing on the relationship between platelets and tumor malignancy.     

Remote Control of the Synthesis of a [2]Rotaxane and its Shuttling via Metal-Ion Translocation

Remote control in an eight-component network commanded both the synthesis and shuttling of a [2]rotaxane via metal-ion translocation, the latter being easily monitored by distinct colorimetric and fluorimetric signals. Addition of zinc(II) ions to the red colored copper-ion relay station rapidly liberated copper(I) ions and afforded the corresponding zinc complex that was visualized by a bright sky blue fluorescence at 460 nm. In a mixture of all eight components of the network, the liberated copper(I) ions were translocated to a macrocycle that catalyzed formation of a rotaxane by a double-click reaction of acetylenic and diazide compounds. The shuttling frequency in the copper-loaded [2]rotaxane was determined to k₂₉₈=30 kHz (ΔH^≠=62.3±0.6 kJ mol⁻¹, ΔS^≠=50.1±5.1 J mol⁻¹ K⁻¹, ΔG^≠₂₉₈=47.4 kJ mol⁻¹). Removal of zinc(II) ions from the mixture reversed the system back generating the metal-free rotaxane. Further alternate addition and removal of Zn²⁺ reversibly controlled the shuttling mode of the rotaxane in this eight-component network where the ion translocation status was monitored by the naked eye.     

NIR‐Triggered Release of Nitric Oxide with Upconversion Nanoparticles Inhibits Platelet Aggregation in Blood Samples

There is a great challenge to overcome the limitation of tissue penetration depth, while maximizing the benefit of light‐triggered biochemical cascades in a well‐defined mode simultaneously. Here, a new method of near‐infrared (NIR) light‐triggered release of nitric oxide (NO) by developing upconversion nanoparticles (UCNPs)‐based conjugate chemistry is reported. As the key nanotransducer in the design, core–shell‐structured UCNPs are encapsulated with a layer of SiO₂ and then covalently linked with a potent NO‐releasing donor (S‐nitroso‐N‐acetyl‐dl ‐penicillamine, SNAP). It is featured with highly localized breakage of chemical bonds of SNAP molecules by NIR–UV upconversion, enabling simultaneous NO release in a light dosage‐dependent manner. The biological effects of NO releasing are demonstrated by cellular imaging and inhibition of platelet aggregation from blood samples. This work provides a flexible and robust platform to generate cell‐signaling gas molecules trigged by NIR laser with deep tissue penetration.