Modifying the DPClus algorithm for identifying protein complexes based on new topological structures

<p>Abstract</p> <p>Background</p> <p>Identification of protein complexes is crucial for understanding principles of cellular organization and functions. As the size of protein-protein interaction set increases, a general trend is to represent the interactions as a network and to develop effective algorithms to detect significant complexes in such networks.</p> <p>Results</p> <p>Based on the study of known complexes in protein networks, this paper proposes a new topological structure for protein complexes, which is a combination of subgraph diameter (or average vertex distance) and subgraph density. Following the approach of that of the previously proposed clustering algorithm DPClus which expands clusters starting from seeded vertices, we present a clustering algorithm IPCA based on the new topological structure for identifying complexes in large protein interaction networks. The algorithm IPCA is applied to the protein interaction network of Sacchromyces cerevisiae and identifies many well known complexes. Experimental results show that the algorithm IPCA recalls more known complexes than previously proposed clustering algorithms, including DPClus, CFinder, LCMA, MCODE, RNSC and STM.</p> <p>Conclusion</p> <p>The proposed algorithm based on the new topological structure makes it possible to identify dense subgraphs in protein interaction networks, many of which correspond to known protein complexes. The algorithm is robust to the known high rate of false positives and false negatives in data from high-throughout interaction techniques. The program is available at <url>http://netlab.csu.edu.cn/bioinformatics/limin/IPCA</url>.</p

1,3-Di-4-pyrid­ylpropane–2-hydroxy­benzene-1,4-dicarboxylic acid (1/2)

In the title compound, C13H14N2·2C8H6O5, which crystallized in the monoclinic C2/c space group, the 1,3-bis­(4-pyrid­yl)propane mol­ecules and 2-hydr­oxy-1,4-benzene­dicarboxylic acid mol­ecules are alternately linked by O—H⋯N and O—H⋯O hydrogen bonds into herringbone/zigzag chains

Molecular dynamics simulation of persistent slip bands formation in nickel-base superalloys

Persistent slip band (PSB) is an important and typical microstructure generated during fatigue crack initiation. Intensive work has been done to investigate the mechanisms of the formation of persistent slip bands since the 1950s when Wadsworth[1] observed the fatigue fracture in copper. Simulations have indicated that PSBs formation during fatigue crack initiation is related to the dislocation driving force and interaction. In this paper, a molecular dynamics (MD) simulation associated with embedded atom model (EAM) is applied to the PSBs formation in nickel-base superalloys with different microstructure and temperature under tensiletensile loadings. Five MD models with different microstructure (pure γ phase and γ/γ′ phase), grain orientation ([1 0 0][0 1 0][0 0 1] and [1 1 1][1 ¯ 0 1][1 2 ¯ 1]) and simulation temperature (300 K, 600 K, 900 K) were built up in these simulations. Our results indicated that within the γ phase by massive dislocations, pile-up and propagation which can penetrate the grain. Also, it is found that the temperature will affect the material fatigue performance and blur PSBs appearance. The simulation results are in strong agreement with published experimental test result. This simulation is based on the work[2]. The highlights of the article include: 1) investigation of the PSB formation via molecular dynamics simulation with three different parameters, 2) conduct of a new deformation and velocity combination controlled simulation for the PSB formation, 3) high-performance computing of PSB formation, and 4) systematic analysis of the PSB formation at the atomic scale in which the dislocation plays a critical role

Characterization of Fam20C expression in odontogenesis and osteogenesis using transgenic mice

Our previous studies have demonstrated that Fam20C promotes differentiation and mineralization of odontoblasts, ameloblasts, osteoblasts and osteocytes during tooth and bone development. Ablation of the Fam20C gene inhibits bone and tooth growth by increasing fibroblast growth factor 23 in serum and causing hypophosphatemia in conditional knockout mice. However, control and regulation of the expression of Fam20C are still unknown. In this study, we generated a transgenic reporter model which expresses green fluorescence protein (GFP) driven by the Fam20C promoter. Recombineering was used to insert a 16 kb fragment of the mouse Fam20C gene (containing the 15 kb promoter and 1.1 kb of exon 1) into a pBluescript SK vector with the topaz variant of GFP and a bovine growth hormone polyadenylation sequence. GFP expression was subsequently evaluated by histomorphometry on cryosections from E14 to adult mice. Fluorescence was evident in the bone and teeth as early as E17.5. The GFP signal was maintained stably in odontoblasts and osteoblasts until 4 weeks after birth. The expression of GFP was significantly reduced in teeth, alveolar bone and muscle by 8 weeks of age. We also observed colocalization of the GFP signal with the Fam20C antibody in postnatal 1- and 7-day-old animals. Successful generation of Fam20C-GFP transgenic mice will provide a unique model for studying Fam20C gene expression and the biological function of this gene during odontogenesis and osteogenesis

Insights into the release of triclosan from microplastics in aquatic environment assessed with diffusive gradient in thin-films

Organic chemicals associated with microplastics (MPs) can be released and thus pose potential risks during weathering processes. However, the thermodynamics and kinetics of their release processes still need to be better understood. Herein, the adsorption and desorption kinetics of triclosan on polystyrene (PS) and polyvinyl chloride (PVC) were investigated by using both batch experiments and diffusive gradients in thin-films (DGT) technique. The pseudo-second-order model fitted the data best, implying that both intraparticle diffusion and external liquid film diffusion influence the adsorption and desorption processes. DGT continuously accumulated triclosan from MP suspensions but slower than theoretical values, indicating some restrictions to desorption. The DGT-induced fluxes in Soils/Sediment (DIFS) model, employed to interpret DGT data, gave distribution coefficients for labile species (K ) of 5000 mL g (PS) and 1000 mL g (PVC) and the corresponding response times (T ) were 10 s and 1000 s, respectively. Higher K but smaller T for PS than PVC showed that more triclosan adsorbed on PS could be rapidly released, while there were some kinetic limitations for triclosan on PVC. A novel finding was that pH and ionic strength individually and interactively affected the supply of triclosan to DGT. This is the first study to quantify interactions of organics with MPs by using DGT, aiding our understanding of MPs' adsorption/desorption behavior in the aquatic environment

Yap1 Hydroxylation Suppress Prostate Cancer Metastasis

View full abstracthttps://openworks.mdanderson.org/leading-edge/1031/thumbnail.jp

Apoptotic Engulfment Pathway and Schizophrenia

Background: Apoptosis has been speculated to be involved in schizophrenia. In a previously study, we reported the association of the MEGF10 gene with the disease. In this study, we followed the apoptotic engulfment pathway involving the MEGF10, GULP1, ABCA1 and ABCA7 genes and tested their association with the disease. Methodology/Principal Findings: Ten, eleven and five SNPs were genotyped in the GULP1, ABCA1 and ABCA7 genes respectively for the ISHDSF and ICCSS samples. In all 3 genes, we observed nominally significant associations. Rs2004888 at GULP1 was significant in both ISHDSF and ICCSS samples (p = 0.0083 and 0.0437 respectively). We sought replication in independent samples for this marker and found highly significant association (p = 0.0003) in 3 Caucasian replication samples. But it was not significant in the 2 Chinese replication samples. In addition, we found a significant 2-marker (rs2242436 * rs3858075) interaction between the ABCA1 and ABCA7 genes in the ISHDSF sample (p = 0.0022) and a 3-marker interaction (rs246896 * rs4522565 * rs3858075) amongst the MEGF10, GULP1 and ABCA1 genes in the ICCSS sample (p = 0.0120). Rs3858075 in the ABCA1 gene was involved in both 2- and 3-marker interactions in the two samples. Conclusions/Significance: From these data, we concluded that the GULP1 gene and the apoptotic engulfment pathway are involved in schizophrenia in subjects of European ancestry and multiple genes in the pathway may interactively increase the risks to the disease. © 2009 Chen et al