Modeling and identification of gene regulatory networks: A Granger causality approach

It is of increasing interest in systems biology to discover gene regulatory networks (GRNs) from time-series genomic data, i.e., to explore the interactions among a large number of genes and gene products over time. Currently, one common approach is based on Granger causality, which models the time-series genomic data as a vector autoregressive (VAR) process and estimates the GRNs from the VAR coefficient matrix. The main challenge for identification of VAR models is the high dimensionality of genes and limited number of time points, which results in statistically inefficient solution and high computational complexity. Therefore, fast and efficient variable selection techniques are highly desirable. In this paper, an introductory review of identification methods and variable selection techniques for VAR models in learning the GRNs will be presented. Furthermore, a dynamic VAR (DVAR) model, which accounts for dynamic GRNs changing with time during the experimental cycle, and its identification methods are introduced. © 2010 IEEE.published_or_final_versionThe 9th International Conference on Machine Learning and Cybernetics (ICMLC 2010), Qingdao, China, 11-14 July 2010. In Proceedings of the 9th ICMLC, 2010, v. 6, p. 3073-307

Genetic diversity among Toxoplasma gondii isolates from different hosts and geographical locations revealed by analysis of ROP13 gene sequences

Toxoplasma gondii can infect almost all the warm-blooded animals and human beings, causing serious public health problems and economic losses worldwide. Rhoptry protein 13 (ROP13) plays some roles in the invasion process of T. gondii. In this study, sequence variation in ROP13 gene among 14 T. gondii isolates from different geographical locations and hosts was examined. The ROP13 gene was amplified from individual isolates and sequenced. Results show that the length of the ROP13 sequences was 1203 bp. In total, there were 44 variable nucleotide positions in the ROP13 sequences, and sequence variations were 0.1 to 2.0% among the 14 examined T. gondii isolates, representing higher rate in transversion than in transition. Intra-specific nucleotide variations were mainly at the second codon positions. Phylogenetic analysis of the 14 examined T. gondii isolates indicate that the ROP13 sequence was not a suitable genetic marker to differentiate T. gondii isolates of different genotypes from different hosts and geographical regions. Low variation in ROP13 gene sequence may suggest that ROP13 gene could represent a good vaccine candidate against toxoplasmosis.Key words: Toxoplasma gondii, toxoplasmosis, rhpotry protein 13 (ROP13), sequence variation, phylogenetic analysis

Sequence variation in TgROP7 gene among Toxoplasma gondii isolates from different hosts and geographical regions

Toxoplasma gondii can infect a wide range of hosts including mammals and birds, causing toxoplasmosis which is one of the most common parasitic zoonoses worldwide. The present study examined sequence variation in rhoptry 7 (ROP7) gene among different T. gondii isolates from different hosts and geographical localities. Phylogenetic analysis of the examined T. gondii isolates was conducted using the maximum likelihood (ML) method. Sequence analysis revealed that 60 nucleotide positions were variable in the ROP7 gene sequences among the 19 examined T. gondii isolates, corresponding to sequence variations of 0 to 1.7%, which occurred at the first, second and third codons. Phylogenetic analysis indicated that sequence variation in ROP7 gene was low among the examined T. gondii isolates from different hosts and geographical localities, and that the ROP7 sequence was not suitable as genetic marker for the differentiation of T. gondii isolates. The results of the present study suggest that ROP7 gene may be a suitable vaccine candidate.Key words: Sequence variation, rhoptry 7 (ROP7) gene, Toxoplasma gondii, toxoplasmosis, phylogenetic analysis

SUMO-2 promotes mRNA translation by enhancing interaction between eIF4E and eIF4G

Small ubiquitin-like modifier (SUMO) proteins regulate many important eukaryotic cellular processes through reversible covalent conjugation to target proteins. In addition to its many well-known biological consequences, like subcellular translocation of protein, subnuclear structure formation, and modulation of transcriptional activity, we show here that SUMO-2 also plays a role in mRNA translation. SUMO-2 promoted formation of the active eukaryotic initiation factor 4F (eIF4F) complex by enhancing interaction between Eukaryotic Initiation Factor 4E (eIF4E) and Eukaryotic Initiation Factor 4G (eIF4G), and induced translation of a subset of proteins, such as cyclinD1 and c-myc, which essential for cell proliferation and apoptosis. As expected, overexpression of SUMO-2 can partially cancel out the disrupting effect of 4EGI-1, a small molecule inhibitor of eIF4E/eIF4G interaction, on formation of the eIF4F complex, translation of the cap-dependent protein, cell proliferation and apoptosis. On the other hand, SUMO-2 knockdown via shRNA partially impaired cap-dependent translation and cell proliferation and promoted apoptosis. These results collectively suggest that SUMO-2 conjugation plays a crucial regulatory role in protein synthesis. Thus, this report might contribute to the basic understanding of mammalian protein translation and sheds some new light on the role of SUMO in this process. © 2014 Chen et al

Coefficient, Distortion and Growth Inequalities for Certain Close-to-Convex Functions

In the present investigation, certain subclasses of close-to-convex functions are investigated. In particular, we obtain an estimate for the Fekete-Szeg\"o functional for functions belonging to the class, distortion, growth estimates and covering theorems

Photoluminescence study on coarsening of self-assembled InAlAs quantum dots on GaAs (001)

Red-emission at similar to 640 nm from self-assembled In0.55Al0.45As/Al0.5Ga0.5As quantum dots grown on GaAs substrate by molecular beam epitaxy (MBE) has been demonstrated. We obtained a double-peak structure of photoluminescence (PL) spectra from quantum dots. An atomic force micrograph (AFM) image for uncapped sample also shows a bimodal distribution of dot sizes. From the temperature and excitation intensity dependence of PL spectra, we found that the double-peak structure of PL spectra from quantum dots was strongly correlated to the two predominant quantum dot families. Taking into account quantum-size effect on the peak energy, we propose that the high (low) energy peak results from a smaller (larger) dot family, and this result is identical with the statistical distribution of dot lateral size from the AFM image

Regulatory T cells in rheumatoid arthritis showed increased plasticity toward Th17 but retained suppressive function in peripheral blood

OBJECTIVE: Regulatory T cells (Tregs) with the plasticity of producing proinflammatory cytokine IL-17 have been demonstrated under normal and pathogenic conditions. However, it remains unclear whether IL-17-producing Tregs lose their suppressive functions because of their plasticity toward Th17 in autoimmunity. The aim of this study was to investigate IL-17-producing Tregs from patients with rheumatoid arthritis (RA), and characterise their regulatory capacity and clinical significance. METHODS: Foxp3 and IL-17 coexpression were evaluated in CD4 T lymphocytes from RA patients. An in vitro T cell polarisation assay was performed to investigate the role of proinflammatory cytokines in IL-17-producing Treg polarisation. The suppressive function of IL-17-producing Tregs in RA was assessed by an in vitro suppression assay. The relationship between this Treg subset and clinical features in RA patients was analysed using Spearman's rank correlation test. RESULTS: A higher frequency of IL-17-producing Tregs was present in the peripheral blood of RA patients compared with healthy subjects. These cells from peripheral blood showed phenotypic characteristics of Th17 and Treg cells, and suppressed T cell proliferation in vitro. Tregs in RA synovial fluid lost suppressive function. The Th17 plasticity of Tregs could be induced by IL-6 and IL-23. An increased ratio of this Treg subset was associated with decreased levels of inflammatory markers, including the erythrocyte sedimentation rate and C-reactive protein level, in patients with RA. CONCLUSIONS: Increased levels of IL-17-producing Tregs were identified in RA patients. This Treg subset with Th17 plasticity in peripheral blood retained suppressive functions and was associated with milder inflammatory conditions, suggesting that this Treg population works as a negative regulator in RA, but in RA synovial site it may be pathogenic.postprin

STUDY ON TOTAL LUMINESCENCE SPECTRA - APPLICATION OF THE MONTE-CARLO METHOD TO 3-DIMENSIONAL SYNCHRONOUS FLUORESCENCE SPECTROMETRY

Three-dimensional synchronous fluorescence spectrometry (TDSFS, a combination of synchronous fluorescence spectrometry and three-dimensional fluorescence spectrometry) is a new method which has been developed recently. The method has usually been used as an efficient tool to select the best Delta lambda value for synchronous fluorescence spectra. This paper studies the sensitivity of the method, which was not been done in the past. The total fluorescence intensity has been used instead of the conventional single point intensity, calculated by the Monte-Carlo method, as the experimental parameter to determine fluorescein and tryptophan. The sensitivity of the total fluorescence method is nearly one hundred times better than that of the single point method. The new method has been used to simultaneously determine naphthalene, pyrene and perylene successfully. The mechanism of the method has also been studied

Strong in-plane optical anisotropy of asymmetric (001) quantum wells

It is well known that asymmetry in the (001) direction can induce in-plane optical anisotropy (IPOA) in (001) quantum wells (QWs). In this letter, asymmetry is introduced in (001) GaAs/AlGaAs QWs by inserting 1 ML (monolayer) of InAs or AlAs at interfaces. Strong IPOA, which is comparable to that in the InGaAs/InP QWs with no common atom, is observed in the asymmetric GaAs/AlGaAs QW by reflectance difference spectroscopy. (C) 2006 American Institute of Physics

Feigenbaum graphs: a complex network perspective of chaos

The recently formulated theory of horizontal visibility graphs transforms time series into graphs and allows the possibility of studying dynamical systems through the characterization of their associated networks. This method leads to a natural graph-theoretical description of nonlinear systems with qualities in the spirit of symbolic dynamics. We support our claim via the case study of the period-doubling and band-splitting attractor cascades that characterize unimodal maps. We provide a universal analytical description of this classic scenario in terms of the horizontal visibility graphs associated with the dynamics within the attractors, that we call Feigenbaum graphs, independent of map nonlinearity or other particulars. We derive exact results for their degree distribution and related quantities, recast them in the context of the renormalization group and find that its fixed points coincide with those of network entropy optimization. Furthermore, we show that the network entropy mimics the Lyapunov exponent of the map independently of its sign, hinting at a Pesin-like relation equally valid out of chaos.Comment: Published in PLoS ONE (Sep 2011