Knowledge-based potentials in protein fold recognition

An accurate potential function is essential for protein folding problem and structure prediction. Two different types of potential energy functions are currently in use. The first type is based on the law of physics and second type is referred to as statistical potentials or knowledge based potentials.  In the latter type, the energy function is extracted from statistical analysis of experimental data of known protein structures. By increasing the amount of three dimensional protein structures, this approach is growing rapidly.There are various forms of knowledge based potentials depending on how statistics are calculated and how proteins are modeled. In this review, we explain how the knowledge based potentials are extracted by using known protein structures and briefly compare many of the potentials in theory

Producción de un genotipo superior a partir de un cultivo de papa agria mediante la variación somaclonal

Este estudio se realizó para producir un genotipo superior de la variedad de papa Agria usando variación somaclonal. Se utilizaron dos explantes de hojas y meristemas en combinación con cuatro dosis de 2,4-D (0, 2, 3 y 4 mg / l) para la inducción de callos en un modelo factorial basado en un diseño completamente al azar con 3 repeticiones. Los resultados mostraron que el explante de meristemo, junto con 3 mg de 2,4-D produjeron los callos más adecuados. En el medio de regeneración mencionado se regeneraron los mejores callos y se seleccionó uno de los genotipos regenerados, que era muy diferente al cultivar parental. El genotipo regenerado, se comparó con el genotipo materno (Agria) y un cultivar control (Sante), en un experimento de campo basado en un diseño de bloques completos al azar con 3 repeticiones. Los resultados mostraron que en términos de la mayoría de los rasgos estudiados, como peso del tubérculo por planta, longitud del estolón, porcentaje de materia seca y porcentaje de almidón, el nuevo genotipo fue superior, en comparación con la variedad parental y en términos de porcentaje de piel y madurez. fecha, el cultivar parental fue superior. Los resultados de la comparación molecular también mostraron que, según el marcador CBDP, tanto en términos de número de banda como de tamaño de banda, había diferencias entre el nuevo genotipo y el cultivar parental. En general, los resultados mostraron que la variación somaclonal puede ser un método eficaz para generar nuevos genotipos con características superiore

IMMAN : an R/Bioconductor package for Interolog protein network reconstruction, mapping and mining analysis

Background: Reconstruction of protein-protein interaction networks (PPIN) has been riddled with controversy for decades. Particularly, false-negative and - positive interactions make this progress even more complicated. Also, lack of a standard PPIN limits us in the comparison studies and results in the incompatible outcomes. Using an evolution-based concept, i.e. interolog which refers to interacting orthologous protein sets, pave the way toward an optimal benchmark. Results: Here, we provide an R package, IMMAN, as a tool for reconstructing Interolog Protein Network (IPN) by integrating several Protein-protein Interaction Networks (PPINs). Users can unify different PPINs to mine conserved common networks among species. IMMAN is designed to retrieve IPNs with different degrees of conservation to engage prediction analysis of protein functions according to their networks. Conclusions: IPN consists of evolutionarily conserved nodes and their related edges regarding low false positive rates, which can be considered as a gold standard network in the contexts of biological network analysis regarding to those PPINs which is derived from.Peer reviewe

Bipartite network models to design combination therapies in acute myeloid leukaemia

Combination therapy is preferred over single-targeted monotherapies for cancer treatment due to its efficiency and safety. However, identifying effective drug combinations costs time and resources. We propose a method for identifying potential drug combinations by bipartite network modelling of patient-related drug response data, specifically the Beat AML dataset. The median of cell viability is used as a drug potency measurement to reconstruct a weighted bipartite network, model drug-biological sample interactions, and find the clusters of nodes inside two projected networks. Then, the clustering results are leveraged to discover effective multi-targeted drug combinations, which are also supported by more evidence using GDSC and ALMANAC databases. The potency and synergy levels of selective drug combinations are corroborated against monotherapy in three cell lines for acute myeloid leukaemia in vitro. In this study, we introduce a nominal data mining approach to improving acute myeloid leukaemia treatment through combinatorial therapy.Peer reviewe

Can We Assume the Gene Expression Profile as a Proxy for Signaling Network Activity?

Studying relationships among gene products by expression profile analysis is a common approach in systems biology. Many studies have generalized the outcomes to the different levels of central dogma information flow and assumed a correlation of transcript and protein expression levels. However, the relation between the various types of interaction (i.e., activation and inhibition) of gene products to their expression profiles has not been widely studied. In fact, looking for any perturbation according to differentially expressed genes is the common approach, while analyzing the effects of altered expression on the activity of signaling pathways is often ignored. In this study, we examine whether significant changes in gene expression necessarily lead to dysregulated signaling pathways. Using four commonly used and comprehensive databases, we extracted all relevant gene expression data and all relationships among directly linked gene pairs. We aimed to evaluate the ratio of coherency or sign consistency between the expression level as well as the causal relationships among the gene pairs. Through a comparison with random unconnected gene pairs, we illustrate that the signaling network is incoherent, and inconsistent with the recorded expression profile. Finally, we demonstrate that, to infer perturbed signaling pathways, we need to consider the type of relationships in addition to gene-product expression data, especially at the transcript level. We assert that identifying enriched biological processes via differentially expressed genes is limited when attempting to infer dysregulated pathways.Peer reviewe

Evaluation of expectation of patients and their parents from orthodontic treatment in babol in 2016-2017

Introduction: The aim of this study was to recognize and investigate the expectations of patients and their parents from orthodontic treatment in order to increase the satisfaction from treatment outcome and enhance the patients’ cooperation in Babol in 2017. Materials & Methods: Totally, 200 people (100 patients aged 12-18 with one of their parents) who were attending for their first orthodontic treatment session participated in this cross-sectional study. Participants completed a self-administered questionnaire which was translated by Forward-Backward method from English to Persian language. Data were analyzed using SPSS 22 through descriptive statistics and t-tests. Results: The most important expectations of patients and their parents from the first appointment of orthodontic treatment were check -up, diagnosis, discussion about treatment, and oral hygiene checking. Patients’ expectations from first appointment were higher than their parents in “brace being fitted” (p=0.001), lower in “have a discussion about treatment plan” (p=0.006), “have x-rays” (p=0.003), and “have oral hygiene checked” (p=0.03). The highest expectation of patients as well as their parents from the type of orthodontic treatment was fixed braces. The main expectation of patients and parents from orthodontic treatment was the demand for straightening teeth and improving aesthetics. Conclusion: Parents than patients had more reasonable expectations from the first appointment of orthodontic treatment. Parents had higher expectations from orthodontic treatment benefits. Age and gender did not have significant effect on the type and level of expectations of parents and patients

Active processes in one dimension

We consider the thermal and athermal overdamped motion of particles in 1D geometries where discrete internal degrees of freedom (spin) are coupled with the translational motion. Adding a driving velocity that depends on the time-dependent spin constitutes the simplest model of active particles (run-and-tumble processes) where the violation of the equipartition principle and of the Sutherland-Einstein relation can be studied in detail even when there is generalized reversibility. We give an example (with four spin values) where the irreversibility of the translational motion manifests itself only in higher-order (than two) time correlations. We derive a generalized telegraph equation as the Smoluchowski equation for the spatial density for an arbitrary number of spin values. We also investigate the Arrhenius exponential law for run-and-tumble particles, due to their activity the slope of the potential becomes important in contrast to the passive diffusion case and activity enhances the escape from a potential well (if that slope is high enough). Finally, in the absence of a driving velocity, the presence of internal currents such as in the chemistry of molecular motors may be transmitted to the translational motion and the internal activity is crucial for the direction of the emerging spatial current.Comment: 26 pages, 3 figure

An insight to HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) pathogenesis; evidence from high-throughput data integration and meta-analysis

Background Human T-lymphotropic virus 1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) is a progressive disease of the central nervous system that significantly affected spinal cord, nevertheless, the pathogenesis pathway and reliable biomarkers have not been well determined. This study aimed to employ high throughput meta-analysis to find major genes that are possibly involved in the pathogenesis of HAM/TSP. Results High-throughput statistical analyses identified 832, 49, and 22 differentially expressed genes for normal vs. ACs, normal vs. HAM/TSP, and ACs vs. HAM/TSP groups, respectively. The protein-protein interactions between DEGs were identified in STRING and further network analyses highlighted 24 and 6 hub genes for normal vs. HAM/TSP and ACs vs. HAM/TSP groups, respectively. Moreover, four biologically meaningful modules including 251 genes were identified for normal vs. ACs. Biological network analyses indicated the involvement of hub genes in many vital pathways like JAK-STAT signaling pathway, interferon, Interleukins, and immune pathways in the normal vs. HAM/TSP group and Metabolism of RNA, Viral mRNA Translation, Human T cell leukemia virus 1 infection, and Cell cycle in the normal vs. ACs group. Moreover, three major genes including STAT1, TAP1, and PSMB8 were identified by network analysis. Real-time PCR revealed the meaningful down-regulation of STAT1 in HAM/TSP samples than AC and normal samples (P = 0.01 and P = 0.02, respectively), up-regulation of PSMB8 in HAM/TSP samples than AC and normal samples (P = 0.04 and P = 0.01, respectively), and down-regulation of TAP1 in HAM/TSP samples than those in AC and normal samples (P = 0.008 and P = 0.02, respectively). No significant difference was found among three groups in terms of the percentage of T helper and cytotoxic T lymphocytes (P = 0.55 and P = 0.12). Conclusions High-throughput data integration disclosed novel hub genes involved in important pathways in virus infection and immune systems. The comprehensive studies are needed to improve our knowledge about the pathogenesis pathways and also biomarkers of complex diseases.Peer reviewe