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Sample records for silico transformation reveals

  1. In silico synchronization reveals regulators of nuclear ruptures in lamin A/C deficient model cells

    PubMed Central

    Robijns, J.; Molenberghs, F.; Sieprath, T.; Corne, T. D. J.; Verschuuren, M.; De Vos, W. H.

    2016-01-01

    The nuclear lamina is a critical regulator of nuclear structure and function. Nuclei from laminopathy patient cells experience repetitive disruptions of the nuclear envelope, causing transient intermingling of nuclear and cytoplasmic components. The exact causes and consequences of these events are not fully understood, but their stochastic occurrence complicates in-depth analyses. To resolve this, we have established a method that enables quantitative investigation of spontaneous nuclear ruptures, based on co-expression of a firmly bound nuclear reference marker and a fluorescent protein that shuttles between the nucleus and cytoplasm during ruptures. Minimally invasive imaging of both reporters, combined with automated tracking and in silico synchronization of individual rupture events, allowed extracting information on rupture frequency and recovery kinetics. Using this approach, we found that rupture frequency correlates inversely with lamin A/C levels, and can be reduced in genome-edited LMNA knockout cells by blocking actomyosin contractility or inhibiting the acetyl-transferase protein NAT10. Nuclear signal recovery followed a kinetic that is co-determined by the severity of the rupture event, and could be prolonged by knockdown of the ESCRT-III complex component CHMP4B. In conclusion, our approach reveals regulators of nuclear rupture induction and repair, which may have critical roles in disease development. PMID:27461848

  2. In silico synchronization reveals regulators of nuclear ruptures in lamin A/C deficient model cells.

    PubMed

    Robijns, J; Molenberghs, F; Sieprath, T; Corne, T D J; Verschuuren, M; De Vos, W H

    2016-01-01

    The nuclear lamina is a critical regulator of nuclear structure and function. Nuclei from laminopathy patient cells experience repetitive disruptions of the nuclear envelope, causing transient intermingling of nuclear and cytoplasmic components. The exact causes and consequences of these events are not fully understood, but their stochastic occurrence complicates in-depth analyses. To resolve this, we have established a method that enables quantitative investigation of spontaneous nuclear ruptures, based on co-expression of a firmly bound nuclear reference marker and a fluorescent protein that shuttles between the nucleus and cytoplasm during ruptures. Minimally invasive imaging of both reporters, combined with automated tracking and in silico synchronization of individual rupture events, allowed extracting information on rupture frequency and recovery kinetics. Using this approach, we found that rupture frequency correlates inversely with lamin A/C levels, and can be reduced in genome-edited LMNA knockout cells by blocking actomyosin contractility or inhibiting the acetyl-transferase protein NAT10. Nuclear signal recovery followed a kinetic that is co-determined by the severity of the rupture event, and could be prolonged by knockdown of the ESCRT-III complex component CHMP4B. In conclusion, our approach reveals regulators of nuclear rupture induction and repair, which may have critical roles in disease development. PMID:27461848

  3. In silico synchronization reveals regulators of nuclear ruptures in lamin A/C deficient model cells

    NASA Astrophysics Data System (ADS)

    Robijns, J.; Molenberghs, F.; Sieprath, T.; Corne, T. D. J.; Verschuuren, M.; de Vos, W. H.

    2016-07-01

    The nuclear lamina is a critical regulator of nuclear structure and function. Nuclei from laminopathy patient cells experience repetitive disruptions of the nuclear envelope, causing transient intermingling of nuclear and cytoplasmic components. The exact causes and consequences of these events are not fully understood, but their stochastic occurrence complicates in-depth analyses. To resolve this, we have established a method that enables quantitative investigation of spontaneous nuclear ruptures, based on co-expression of a firmly bound nuclear reference marker and a fluorescent protein that shuttles between the nucleus and cytoplasm during ruptures. Minimally invasive imaging of both reporters, combined with automated tracking and in silico synchronization of individual rupture events, allowed extracting information on rupture frequency and recovery kinetics. Using this approach, we found that rupture frequency correlates inversely with lamin A/C levels, and can be reduced in genome-edited LMNA knockout cells by blocking actomyosin contractility or inhibiting the acetyl-transferase protein NAT10. Nuclear signal recovery followed a kinetic that is co-determined by the severity of the rupture event, and could be prolonged by knockdown of the ESCRT-III complex component CHMP4B. In conclusion, our approach reveals regulators of nuclear rupture induction and repair, which may have critical roles in disease development.

  4. Directed evolution and in silico analysis of reaction centre proteins reveal molecular signatures of photosynthesis adaptation to radiation pressure.

    PubMed

    Rea, Giuseppina; Lambreva, Maya; Polticelli, Fabio; Bertalan, Ivo; Antonacci, Amina; Pastorelli, Sandro; Damasso, Mario; Johanningmeier, Udo; Giardi, Maria Teresa

    2011-01-01

    Evolutionary mechanisms adopted by the photosynthetic apparatus to modifications in the Earth's atmosphere on a geological time-scale remain a focus of intense research. The photosynthetic machinery has had to cope with continuously changing environmental conditions and particularly with the complex ionizing radiation emitted by solar flares. The photosynthetic D1 protein, being the site of electron tunneling-mediated charge separation and solar energy transduction, is a hot spot for the generation of radiation-induced radical injuries. We explored the possibility to produce D1 variants tolerant to ionizing radiation in Chlamydomonas reinhardtii and clarified the effect of radiation-induced oxidative damage on the photosynthetic proteins evolution. In vitro directed evolution strategies targeted at the D1 protein were adopted to create libraries of chlamydomonas random mutants, subsequently selected by exposures to radical-generating proton or neutron sources. The common trend observed in the D1 aminoacidic substitutions was the replacement of less polar by more polar amino acids. The applied selection pressure forced replacement of residues more sensitive to oxidative damage with less sensitive ones, suggesting that ionizing radiation may have been one of the driving forces in the evolution of the eukaryotic photosynthetic apparatus. A set of the identified aminoacidic substitutions, close to the secondary plastoquinone binding niche and oxygen evolving complex, were introduced by site-directed mutagenesis in un-transformed strains, and their sensitivity to free radicals attack analyzed. Mutants displayed reduced electron transport efficiency in physiological conditions, and increased photosynthetic performance stability and oxygen evolution capacity in stressful high-light conditions. Finally, comparative in silico analyses of D1 aminoacidic sequences of organisms differently located in the evolution chain, revealed a higher ratio of residues more sensitive to

  5. Directed Evolution and In Silico Analysis of Reaction Centre Proteins Reveal Molecular Signatures of Photosynthesis Adaptation to Radiation Pressure

    PubMed Central

    Rea, Giuseppina; Lambreva, Maya; Polticelli, Fabio; Bertalan, Ivo; Antonacci, Amina; Pastorelli, Sandro; Damasso, Mario; Johanningmeier, Udo; Giardi, Maria Teresa

    2011-01-01

    Evolutionary mechanisms adopted by the photosynthetic apparatus to modifications in the Earth's atmosphere on a geological time-scale remain a focus of intense research. The photosynthetic machinery has had to cope with continuously changing environmental conditions and particularly with the complex ionizing radiation emitted by solar flares. The photosynthetic D1 protein, being the site of electron tunneling-mediated charge separation and solar energy transduction, is a hot spot for the generation of radiation-induced radical injuries. We explored the possibility to produce D1 variants tolerant to ionizing radiation in Chlamydomonas reinhardtii and clarified the effect of radiation-induced oxidative damage on the photosynthetic proteins evolution. In vitro directed evolution strategies targeted at the D1 protein were adopted to create libraries of chlamydomonas random mutants, subsequently selected by exposures to radical-generating proton or neutron sources. The common trend observed in the D1 aminoacidic substitutions was the replacement of less polar by more polar amino acids. The applied selection pressure forced replacement of residues more sensitive to oxidative damage with less sensitive ones, suggesting that ionizing radiation may have been one of the driving forces in the evolution of the eukaryotic photosynthetic apparatus. A set of the identified aminoacidic substitutions, close to the secondary plastoquinone binding niche and oxygen evolving complex, were introduced by site-directed mutagenesis in un-transformed strains, and their sensitivity to free radicals attack analyzed. Mutants displayed reduced electron transport efficiency in physiological conditions, and increased photosynthetic performance stability and oxygen evolution capacity in stressful high-light conditions. Finally, comparative in silico analyses of D1 aminoacidic sequences of organisms differently located in the evolution chain, revealed a higher ratio of residues more sensitive to

  6. Molecular Docking and In Silico ADMET Study Reveals Acylguanidine 7a as a Potential Inhibitor of β-Secretase.

    PubMed

    Nisha, Chaluveelaveedu Murleedharan; Kumar, Ashwini; Nair, Prateek; Gupta, Nityasha; Silakari, Chitrangda; Tripathi, Timir; Kumar, Awanish

    2016-01-01

    Amyloidogenic pathway in Alzheimer's disease (AD) involves breakdown of APP by β-secretase followed by γ-secretase and results in formation of amyloid beta plaque. β-secretase has been a promising target for developing novel anti-Alzheimer drugs. To test different molecules for this purpose, test ligands like acylguanidine 7a, rosiglitazone, pioglitazone, and tartaric acid were docked against our target protein β-secretase enzyme retrieved from Protein Data Bank, considering MK-8931 (phase III trial, Merck) as the positive control. Docking revealed that, with respect to their free binding energy, acylguanidine 7a has the lowest binding energy followed by MK-8931 and pioglitazone and binds significantly to β-secretase. In silico ADMET predictions revealed that except tartaric acid all other compounds had minimal toxic effects and had good absorption as well as solubility characteristics. These compounds may serve as potential lead compound for developing new anti-Alzheimer drug. PMID:27190510

  7. Molecular Docking and In Silico ADMET Study Reveals Acylguanidine 7a as a Potential Inhibitor of β-Secretase

    PubMed Central

    Nisha, Chaluveelaveedu Murleedharan; Kumar, Ashwini; Nair, Prateek; Gupta, Nityasha; Silakari, Chitrangda; Tripathi, Timir; Kumar, Awanish

    2016-01-01

    Amyloidogenic pathway in Alzheimer's disease (AD) involves breakdown of APP by β-secretase followed by γ-secretase and results in formation of amyloid beta plaque. β-secretase has been a promising target for developing novel anti-Alzheimer drugs. To test different molecules for this purpose, test ligands like acylguanidine 7a, rosiglitazone, pioglitazone, and tartaric acid were docked against our target protein β-secretase enzyme retrieved from Protein Data Bank, considering MK-8931 (phase III trial, Merck) as the positive control. Docking revealed that, with respect to their free binding energy, acylguanidine 7a has the lowest binding energy followed by MK-8931 and pioglitazone and binds significantly to β-secretase. In silico ADMET predictions revealed that except tartaric acid all other compounds had minimal toxic effects and had good absorption as well as solubility characteristics. These compounds may serve as potential lead compound for developing new anti-Alzheimer drug. PMID:27190510

  8. In silico pathway analysis in cervical carcinoma reveals potential new targets for treatment

    PubMed Central

    van Dam, Peter A.; van Dam, Pieter-Jan H. H.; Rolfo, Christian; Giallombardo, Marco; van Berckelaer, Christophe; Trinh, Xuan Bich; Altintas, Sevilay; Huizing, Manon; Papadimitriou, Kostas; Tjalma, Wiebren A. A.; van Laere, Steven

    2016-01-01

    An in silico pathway analysis was performed in order to improve current knowledge on the molecular drivers of cervical cancer and detect potential targets for treatment. Three publicly available Affymetrix gene expression data-sets (GSE5787, GSE7803, GSE9750) were retrieved, vouching for a total of 9 cervical cancer cell lines (CCCLs), 39 normal cervical samples, 7 CIN3 samples and 111 cervical cancer samples (CCSs). Predication analysis of microarrays was performed in the Affymetrix sets to identify cervical cancer biomarkers. To select cancer cell-specific genes the CCSs were compared to the CCCLs. Validated genes were submitted to a gene set enrichment analysis (GSEA) and Expression2Kinases (E2K). In the CCSs a total of 1,547 probe sets were identified that were overexpressed (FDR < 0.1). Comparing to CCCLs 560 probe sets (481 unique genes) had a cancer cell-specific expression profile, and 315 of these genes (65%) were validated. GSEA identified 5 cancer hallmarks enriched in CCSs (P < 0.01 and FDR < 0.25) showing that deregulation of the cell cycle is a major component of cervical cancer biology. E2K identified a protein-protein interaction (PPI) network of 162 nodes (including 20 drugable kinases) and 1626 edges. This PPI-network consists of 5 signaling modules associated with MYC signaling (Module 1), cell cycle deregulation (Module 2), TGFβ-signaling (Module 3), MAPK signaling (Module 4) and chromatin modeling (Module 5). Potential targets for treatment which could be identified were CDK1, CDK2, ABL1, ATM, AKT1, MAPK1, MAPK3 among others. The present study identified important driver pathways in cervical carcinogenesis which should be assessed for their potential therapeutic drugability. PMID:26701206

  9. In silico pathway analysis in cervical carcinoma reveals potential new targets for treatment.

    PubMed

    van Dam, Peter A; van Dam, Pieter-Jan H H; Rolfo, Christian; Giallombardo, Marco; van Berckelaer, Christophe; Trinh, Xuan Bich; Altintas, Sevilay; Huizing, Manon; Papadimitriou, Kostas; Tjalma, Wiebren A A; van Laere, Steven

    2016-01-19

    An in silico pathway analysis was performed in order to improve current knowledge on the molecular drivers of cervical cancer and detect potential targets for treatment. Three publicly available Affymetrix gene expression data-sets (GSE5787, GSE7803, GSE9750) were retrieved, vouching for a total of 9 cervical cancer cell lines (CCCLs), 39 normal cervical samples, 7 CIN3 samples and 111 cervical cancer samples (CCSs). Predication analysis of microarrays was performed in the Affymetrix sets to identify cervical cancer biomarkers. To select cancer cell-specific genes the CCSs were compared to the CCCLs. Validated genes were submitted to a gene set enrichment analysis (GSEA) and Expression2Kinases (E2K). In the CCSs a total of 1,547 probe sets were identified that were overexpressed (FDR < 0.1). Comparing to CCCLs 560 probe sets (481 unique genes) had a cancer cell-specific expression profile, and 315 of these genes (65%) were validated. GSEA identified 5 cancer hallmarks enriched in CCSs (P < 0.01 and FDR < 0.25) showing that deregulation of the cell cycle is a major component of cervical cancer biology. E2K identified a protein-protein interaction (PPI) network of 162 nodes (including 20 drugable kinases) and 1626 edges. This PPI-network consists of 5 signaling modules associated with MYC signaling (Module 1), cell cycle deregulation (Module 2), TGFβ-signaling (Module 3), MAPK signaling (Module 4) and chromatin modeling (Module 5). Potential targets for treatment which could be identified were CDK1, CDK2, ABL1, ATM, AKT1, MAPK1, MAPK3 among others. The present study identified important driver pathways in cervical carcinogenesis which should be assessed for their potential therapeutic drugability. PMID:26701206

  10. In silico approach to reveal viral populations in grapevine cultivar Tannat using transcriptome data

    PubMed Central

    Jo, Yeonhwa; Choi, Hoseong; Kyong Cho, Jin; Yoon, Ju-Yeon; Choi, Seung-Kook; Kyong Cho, Won

    2015-01-01

    Viruses are ubiquitous and present in a wide range of settings, from living organisms to various environments. Although viruses are regarded as important pathogens in higher plants, viral populations in specific host plants have not yet been fully examined. This study revealed viral populations in grape berries obtained from a cultivar from a single vineyard using currently available grapevine transcriptomes. Eight viruses and two viroids were identified using 11 grapevine libraries. Virus-associated sequences in each transcriptome ranged from 0.2% (seed) to 8.8% (skin). The amount of viral RNAs and virus copy numbers was quantified, thus revealing the dominant virus or viroid in each individual library. In addition, five viral genomes were successfully assembled de novo using transcriptome data. Phylogenetic analyses revealed that the viruses and viroids might have originated from Europe, along with the host. Single nucleotide variation studies revealed the quasispecies of RNA viruses. Taken together, this study defines complex viral populations in three different grape tissues from a single vineyard. PMID:26508692

  11. In silico approach to reveal viral populations in grapevine cultivar Tannat using transcriptome data.

    PubMed

    Jo, Yeonhwa; Choi, Hoseong; Cho, Jin Kyong; Yoon, Ju-Yeon; Choi, Seung-Kook; Cho, Won Kyong

    2015-01-01

    Viruses are ubiquitous and present in a wide range of settings, from living organisms to various environments. Although viruses are regarded as important pathogens in higher plants, viral populations in specific host plants have not yet been fully examined. This study revealed viral populations in grape berries obtained from a cultivar from a single vineyard using currently available grapevine transcriptomes. Eight viruses and two viroids were identified using 11 grapevine libraries. Virus-associated sequences in each transcriptome ranged from 0.2% (seed) to 8.8% (skin). The amount of viral RNAs and virus copy numbers was quantified, thus revealing the dominant virus or viroid in each individual library. In addition, five viral genomes were successfully assembled de novo using transcriptome data. Phylogenetic analyses revealed that the viruses and viroids might have originated from Europe, along with the host. Single nucleotide variation studies revealed the quasispecies of RNA viruses. Taken together, this study defines complex viral populations in three different grape tissues from a single vineyard. PMID:26508692

  12. In silico analysis of bacterial arsenic islands reveals remarkable synteny and functional relatedness between arsenate and phosphate

    PubMed Central

    Li, Hang; Li, Mingshun; Huang, Yinyan; Rensing, Christopher; Wang, Gejiao

    2013-01-01

    In order to construct a more universal model for understanding the genetic requirements for bacterial AsIII oxidation, an in silico examination of the available sequences in the GenBank was assessed and revealed 21 conserved 5–71 kb arsenic islands within phylogenetically diverse bacterial genomes. The arsenic islands included the AsIII oxidase structural genes aioBA, ars operons (e.g., arsRCB) which code for arsenic resistance, and pho, pst, and phn genes known to be part of the classical phosphate stress response and that encode functions associated with regulating and acquiring organic and inorganic phosphorus. The regulatory genes aioXSR were also an island component, but only in Proteobacteria and orientated differently depending on whether they were in α-Proteobacteria or β-/γ-Proteobacteria. Curiously though, while these regulatory genes have been shown to be essential to AsIII oxidation in the Proteobacteria, they are absent in most other organisms examined, inferring different regulatory mechanism(s) yet to be discovered. Phylogenetic analysis of the aio, ars, pst, and phn genes revealed evidence of both vertical inheritance and horizontal gene transfer (HGT). It is therefore likely the arsenic islands did not evolve as a whole unit but formed independently by acquisition of functionally related genes and operons in respective strains. Considering gene synteny and structural analogies between arsenate and phosphate, we presumed that these genes function together in helping these microbes to be able to use even low concentrations of phosphorus needed for vital functions under high concentrations of arsenic, and defined these sequences as the arsenic islands. PMID:24312089

  13. In silico modeling of spore inhalation reveals fungal persistence following low dose exposure

    PubMed Central

    Tanaka, Reiko J.; Boon, Neville J.; Vrcelj, Katarina; Nguyen, Anita; Vinci, Carmelina; Armstrong-James, Darius; Bignell, Elaine

    2015-01-01

    The human lung is constantly exposed to spores of the environmental mould Aspergillus fumigatus, a major opportunistic pathogen. The spectrum of resultant disease is the outcome of complex host-pathogen interactions, an integrated, quantitative understanding of which lies beyond the ethical and technical reach permitted by animal studies. Here we construct a mathematical model of spore inhalation and clearance by concerted actions of macrophages and neutrophils, and use it to derive a mechanistic understanding of pathogen clearance by the healthy, immunocompetent host. In particular, we investigated the impact of inoculum size upon outcomes of single-dose fungal exposure by simulated titrations of inoculation dose, from 106 to 102 spores. Simulated low-dose (102) spore exposure, an everyday occurrence for humans, revealed a counter-intuitive prediction of fungal persistence (>3 days). The model predictions were reflected in the short-term dynamics of experimental murine exposure to fungal spores, thereby highlighting the potential of mathematical modelling for studying relevant behaviours in experimental models of fungal disease. Our model suggests that infectious outcomes can be highly dependent upon short-term dynamics of fungal exposure, which may govern occurrence of cyclic or persistent subclinical fungal colonisation of the lung following low dose spore inhalation in non-neutropenic hosts. PMID:26364644

  14. In Silico analysis of Gastric carcinoma Serial Analysis of Gene Expression libraries reveals different profiles associated with ethnicity

    PubMed Central

    Ossandon, Francisco J; Villarroel, Cynthia; Aguayo, Francisco; Santibanez, Eudocia; Oue, Naohide; Yasui, Wataru; Corvalan, Alejandro H

    2008-01-01

    Worldwide gastric carcinoma has marked geographical variations and worse outcome in patients from the West compared to the East. Although these differences has been explained by better diagnostic criteria, improved staging methods and more radical surgery, emerging evidence supports the concept that gene expression differences associated to ethnicity might contribute to this disparate outcome. Here, we collected datasets from 4 normal and 11 gastric carcinoma Serial Gene Expression Analysis (SAGE) libraries from two different ethnicities. All normal SAGE libraries as well as 7 tumor libraries were from the West and 4 tumor libraries were from the East. These datasets we compare by Correspondence Analysis and Support Tree analysis and specific differences in tags expression were identified by Significance Analysis for Microarray. Tags to gene assignments were performed by CGAP-SAGE Genie or TAGmapper. The analysis of global transcriptome shows a clear separation between normal and tumor libraries with 90 tags differentially expressed. A clear separation was also found between the West and the East tumor libraries with 54 tags differentially expressed. Tags to gene assignments identified 15 genes, 5 of them with significant higher expression in the West libraries in comparison to the East libraries. qRT-PCR in cell lines from west and east origin confirmed these differences. Interestingly, two of these genes have been associated to aggressiveness (COL1A1 and KLK10). In conclusion we found that in silico analysis of SAGE libraries from two different ethnicities reveal differences in gene expression profile. These expression differences might contribute to explain the disparate outcome between the West and the East. PMID:18302799

  15. Quantitative X-ray Diffraction (QXRD) analysis for revealing thermal transformations of red mud.

    PubMed

    Liao, Chang-Zhong; Zeng, Lingmin; Shih, Kaimin

    2015-07-01

    Red mud is a worldwide environmental problem, and many authorities are trying to find an economic solution for its beneficial application or/and safe disposal. Ceramic production is one of the potential waste-to-resource strategies for using red mud as a raw material. Before implementing such a strategy, an unambiguous understanding of the reaction behavior of red mud under thermal conditions is essential. In this study, the phase compositions and transformation processes were revealed for the Pingguo red mud (PRM) heat-treated at different sintering temperatures. Hematite, perovskite, andradite, cancrinite, kaolinite, diaspore, gibbsite and calcite phases were observed in the samples. However, unlike those red mud samples from the other regions, no TiO2 (rutile or anatase) or quartz were observed. Titanium was found to exist mainly in perovskite and andradite while the iron mainly existed in hematite and andradite. A new silico-ferrite of calcium and aluminum (SFCA) phase was found in samples treated at temperatures above 1100°C, and two possible formation pathways for SFCA were suggested. This is the first SFCA phase to be reported in thermally treated red mud, and this finding may turn PRM waste into a material resource for the iron-making industry. Titanium was found to be enriched in the perovskite phase after 1200°C thermal treatment, and this observation indicated a potential strategy for the recovery of titanium from PRM. In addition to noting these various resource recovery opportunities, this is also the first study to quantitatively summarize the reaction details of PRM phase transformations at various temperatures. PMID:25841072

  16. Revealing Medicinal Plants That Are Useful for the Comprehensive Management of Epilepsy and Associated Comorbidities through In Silico Mining of Their Phytochemical Diversity.

    PubMed

    Goel, Rajesh Kumar; Gawande, Dinesh; Lagunin, Alexey; Randhawa, Puneet; Mishra, Awanish; Poroikov, Vladimir

    2015-04-01

    In silico techniques in drug discovery may rationalise and speed up the identification of lead molecules from nature. Drug discovery from medicinal plants has mostly been confined to indications in accordance with their ethnical use only. However, the availability of multiple phytoconstituents in medicinal plants suggests that these may be much more useful beyond their traditional uses and in the management of chronic diseases, along with their comorbidities. In this study, the computer programmes PASS and PharmaExpert were used to reveal the medicinal plants useful in the comprehensive management of epilepsy and associated psychiatric disorders based on the pleiotropic effects predicted for their phytoconstituents. In silico analysis revealed that seven of 50 medicinal plants from traditional Indian medicine possessed the desired pleiotropic effect, i.e., anticonvulsant, antidepressant, and nootropic activities. The majority of phytoconstituents from Passiflora incarnata were concurrently predicted to have the desired pleiotropic effects. Therefore, P. incarnata was pharmacologically validated using the pentylenetetrazole kindling mouse model. Behavioural and neurochemical evaluations confirmed the ameliorative role of P. incarnata in epilepsy and the associated depression and memory deficit. The pharmacological findings from this study propose that PASS and PharmaExpert may serve as good tools for the optimisation of the selection of plants based on their phytoconstituents for the treatment of different ailments, even beyond their traditional use. PMID:25856437

  17. In silico activity profiling reveals the mechanism of action of antimalarials discovered in a high-throughput screen

    PubMed Central

    Plouffe, David; Brinker, Achim; McNamara, Case; Henson, Kerstin; Kato, Nobutaka; Kuhen, Kelli; Nagle, Advait; Adrián, Francisco; Matzen, Jason T.; Anderson, Paul; Nam, Tae-gyu; Gray, Nathanael S.; Chatterjee, Arnab; Janes, Jeff; Yan, S. Frank; Trager, Richard; Caldwell, Jeremy S.; Schultz, Peter G.; Zhou, Yingyao; Winzeler, Elizabeth A.

    2008-01-01

    The growing resistance to current first-line antimalarial drugs represents a major health challenge. To facilitate the discovery of new antimalarials, we have implemented an efficient and robust high-throughput cell-based screen (1,536-well format) based on proliferation of Plasmodium falciparum (Pf) in erythrocytes. From a screen of ≈1.7 million compounds, we identified a diverse collection of ≈6,000 small molecules comprised of >530 distinct scaffolds, all of which show potent antimalarial activity (<1.25 μM). Most known antimalarials were identified in this screen, thus validating our approach. In addition, we identified many novel chemical scaffolds, which likely act through both known and novel pathways. We further show that in some cases the mechanism of action of these antimalarials can be determined by in silico compound activity profiling. This method uses large datasets from unrelated cellular and biochemical screens and the guilt-by-association principle to predict which cellular pathway and/or protein target is being inhibited by select compounds. In addition, the screening method has the potential to provide the malaria community with many new starting points for the development of biological probes and drugs with novel antiparasitic activities. PMID:18579783

  18. In Silico Modeling of Liver Metabolism in a Human Disease Reveals a Key Enzyme for Histidine and Histamine Homeostasis.

    PubMed

    Pagliarini, Roberto; Castello, Raffaele; Napolitano, Francesco; Borzone, Roberta; Annunziata, Patrizia; Mandrile, Giorgia; De Marchi, Mario; Brunetti-Pierri, Nicola; di Bernardo, Diego

    2016-06-01

    Primary hyperoxaluria type I (PH1) is an autosomal-recessive inborn error of liver metabolism caused by alanine:glyoxylate aminotransferase (AGT) deficiency. In silico modeling of liver metabolism in PH1 recapitulated accumulation of known biomarkers as well as alteration of histidine and histamine levels, which we confirmed in vitro, in vivo, and in PH1 patients. AGT-deficient mice showed decreased vascular permeability, a readout of in vivo histamine activity. Histamine reduction is most likely caused by increased catabolism of the histamine precursor histidine, triggered by rerouting of alanine flux from AGT to the glutamic-pyruvate transaminase (GPT, also known as the alanine-transaminase ALT). Alanine administration reduces histamine levels in wild-type mice, while overexpression of GPT in PH1 mice increases plasma histidine, normalizes histamine levels, restores vascular permeability, and decreases urinary oxalate levels. Our work demonstrates that genome-scale metabolic models are clinically relevant and can link genotype to phenotype in metabolic disorders. PMID:27239044

  19. An in silico Approach Reveals Associations between Genetic and Epigenetic Factors within Regulatory Elements in B Cells from Primary Sjögren's Syndrome Patients.

    PubMed

    Konsta, Orsia D; Le Dantec, Christelle; Charras, Amandine; Brooks, Wesley H; Arleevskaya, Marina I; Bordron, Anne; Renaudineau, Yves

    2015-01-01

    Recent advances in genetics have highlighted several regions and candidate genes associated with primary Sjögren's syndrome (SS), a systemic autoimmune epithelitis that combines exocrine gland dysfunctions, and focal lymphocytic infiltrations. In addition to genetic factors, it is now clear that epigenetic deregulations are present during SS and restricted to specific cell type subsets, such as lymphocytes and salivary gland epithelial cells. In this study, 72 single nucleotide polymorphisms (SNPs) associated with 43 SS gene risk factors were selected from publicly available and peer reviewed literature for further in silico analysis. SS risk variant location was tested revealing a broad distribution in coding sequences (5.6%), intronic sequences (55.6%), upstream/downstream genic regions (30.5%), and intergenic regions (8.3%). Moreover, a significant enrichment of regulatory motifs (promoter, enhancer, insulator, DNAse peak, and expression quantitative trait loci) characterizes SS risk variants (94.4%). Next, screening SNPs in high linkage disequilibrium (r (2) ≥ 0.8 in Caucasians) revealed 645 new variants including 5 SNPs with missense mutations, and indicated an enrichment of transcriptionally active motifs according to the cell type (B cells > monocytes > T cells ≫ A549). Finally, we looked at SS risk variants for histone markers in B cells (GM12878), monocytes (CD14(+)) and epithelial cells (A548). Active histone markers were associated with SS risk variants at both promoters and enhancers in B cells, and within enhancers in monocytes. In conclusion and based on the obtained in silico results that need further confirmation, associations were observed between SS genetic risk factors and epigenetic factors and these associations predominate in B cells, such as those observed at the FAM167A-BLK locus. PMID:26379672

  20. In silico modelling of prostacyclin and other lipid mediators to nuclear receptors reveal novel thyroid hormone receptor antagonist properties.

    PubMed

    Perez Diaz, Noelia; Zloh, Mire; Patel, Pryank; Mackenzie, Louise S

    2016-01-01

    Prostacyclin (PGI2) is a key mediator involved in cardiovascular homeostasis, acting predominantly on two receptor types; cell surface IP receptor and cytosolic peroxisome proliferator activated receptor (PPAR) β/δ. Having a very short half-life, direct methods to determine its long term effects on cells is difficult, and little is known of its interactions with nuclear receptors. Here we used computational chemistry methods to investigate the potential for PGI2, beraprost (IP receptor agonist), and GW0742 (PPARβ/δ agonist), to bind to nuclear receptors, confirmed with pharmacological methods. In silico screening predicted that PGI2, beraprost, and GW0742 have the potential to bind to different nuclear receptors, in particular thyroid hormone β receptor (TRβ) and thyroid hormone α receptor (TRα). Docking analysis predicts a binding profile to residues thought to have allosteric control on the TR ligand binding site. Luciferase reporter assays confirmed that beraprost and GW0742 display TRβ and TRα antagonistic properties; beraprost IC50 6.3×10(-5)mol/L and GW0742 IC50 4.9×10(-6)mol/L. Changes to triiodothyronine (T3) induced vasodilation of rat mesenteric arteries measured on the wire myograph were measured in the presence of the TR antagonist MLS000389544 (10(-5)mol/L), beraprost (10(-5)mol/L) and GW0742 (10(-5)mol/L); all significantly inhibited T3 induced vasodilation compared to controls. We have shown that both beraprost and GW0742 exhibit TRβ and TRα antagonist behaviour, and suggests that PGI2 has the ability to affect the long term function of cells through binding to and inactivating thyroid hormone receptors. PMID:26686607

  1. Integrated in silico Analyses of Regulatory and Metabolic Networks of Synechococcus sp. PCC 7002 Reveal Relationships between Gene Centrality and Essentiality

    PubMed Central

    Song, Hyun-Seob; McClure, Ryan S.; Bernstein, Hans C.; Overall, Christopher C.; Hill, Eric A.; Beliaev, Alexander S.

    2015-01-01

    Cyanobacteria dynamically relay environmental inputs to intracellular adaptations through a coordinated adjustment of photosynthetic efficiency and carbon processing rates. The output of such adaptations is reflected through changes in transcriptional patterns and metabolic flux distributions that ultimately define growth strategy. To address interrelationships between metabolism and regulation, we performed integrative analyses of metabolic and gene co-expression networks in a model cyanobacterium, Synechococcus sp. PCC 7002. Centrality analyses using the gene co-expression network identified a set of key genes, which were defined here as “topologically important.” Parallel in silico gene knock-out simulations, using the genome-scale metabolic network, classified what we termed as “functionally important” genes, deletion of which affected growth or metabolism. A strong positive correlation was observed between topologically and functionally important genes. Functionally important genes exhibited variable levels of topological centrality; however, the majority of topologically central genes were found to be functionally essential for growth. Subsequent functional enrichment analysis revealed that both functionally and topologically important genes in Synechococcus sp. PCC 7002 are predominantly associated with translation and energy metabolism, two cellular processes critical for growth. This research demonstrates how synergistic network-level analyses can be used for reconciliation of metabolic and gene expression data to uncover fundamental biological principles. PMID:25826650

  2. Integrated in silico analyses of regulatory and metabolic networks of Synechococcus sp. PCC 7002 reveal relationships between gene centrality and essentiality

    SciTech Connect

    Song, Hyun-Seob; McClure, Ryan S.; Bernstein, Hans C.; Overall, Christopher C.; Hill, Eric A.; Beliaev, Alex S.

    2015-03-27

    Cyanobacteria dynamically relay environmental inputs to intracellular adaptations through a coordinated adjustment of photosynthetic efficiency and carbon processing rates. The output of such adaptations is reflected through changes in transcriptional patterns and metabolic flux distributions that ultimately define growth strategy. To address interrelationships between metabolism and regulation, we performed integrative analyses of metabolic and gene co-expression networks in a model cyanobacterium, Synechococcus sp. PCC 7002. Centrality analyses using the gene co-expression network identified a set of key genes, which were defined here as ‘topologically important.’ Parallel in silico gene knock-out simulations, using the genome-scale metabolic network, classified what we termed as ‘functionally important’ genes, deletion of which affected growth or metabolism. A strong positive correlation was observed between topologically and functionally important genes. Functionally important genes exhibited variable levels of topological centrality; however, the majority of topologically central genes were found to be functionally essential for growth. Subsequent functional enrichment analysis revealed that both functionally and topologically important genes in Synechococcus sp. PCC 7002 are predominantly associated with translation and energy metabolism, two cellular processes critical for growth. This research demonstrates how synergistic network-level analyses can be used for reconciliation of metabolic and gene expression data to uncover fundamental biological principles.

  3. Integrated in silico analyses of regulatory and metabolic networks of Synechococcus sp. PCC 7002 reveal relationships between gene centrality and essentiality

    DOE PAGESBeta

    Song, Hyun-Seob; McClure, Ryan S.; Bernstein, Hans C.; Overall, Christopher C.; Hill, Eric A.; Beliaev, Alex S.

    2015-03-27

    Cyanobacteria dynamically relay environmental inputs to intracellular adaptations through a coordinated adjustment of photosynthetic efficiency and carbon processing rates. The output of such adaptations is reflected through changes in transcriptional patterns and metabolic flux distributions that ultimately define growth strategy. To address interrelationships between metabolism and regulation, we performed integrative analyses of metabolic and gene co-expression networks in a model cyanobacterium, Synechococcus sp. PCC 7002. Centrality analyses using the gene co-expression network identified a set of key genes, which were defined here as ‘topologically important.’ Parallel in silico gene knock-out simulations, using the genome-scale metabolic network, classified what we termedmore » as ‘functionally important’ genes, deletion of which affected growth or metabolism. A strong positive correlation was observed between topologically and functionally important genes. Functionally important genes exhibited variable levels of topological centrality; however, the majority of topologically central genes were found to be functionally essential for growth. Subsequent functional enrichment analysis revealed that both functionally and topologically important genes in Synechococcus sp. PCC 7002 are predominantly associated with translation and energy metabolism, two cellular processes critical for growth. This research demonstrates how synergistic network-level analyses can be used for reconciliation of metabolic and gene expression data to uncover fundamental biological principles.« less

  4. In silico analysis of missense mutations in LPAR6 reveals abnormal phospholipid signaling pathway leading to hypotrichosis.

    PubMed

    Raza, Syed Irfan; Muhammad, Dost; Jan, Abid; Ali, Raja Hussain; Hassan, Mubashir; Ahmad, Wasim; Rashid, Sajid

    2014-01-01

    Autosomal recessive hypotrichosis is a rare genetic irreversible hair loss disorder characterized by sparse scalp hair, sparse to absent eyebrows and eyelashes, and sparse axillary and body hair. The study, presented here, established genetic linkage in four families showing similar phenotypes to lysophosphatidic acid receptor 6 (LPAR6) gene on chromosome 13q14.11-q21.32. Subsequently, sequence analysis of the gene revealed two previously reported missense mutations including p.D63V in affected members of one and p.I188F in three other families. Molecular modeling and docking analysis was performed to investigate binding of a ligand oleoyl-L-alpha-lysophosphatidic acid (LPA) to modeled protein structures of normal and mutated (D63V, G146R, I188F, N248Y, S3T, L277P) LPAR6 receptors. The mutant receptors showed a complete shift in orientation of LPA at the binding site. In addition, hydropathy analysis revealed a significant change in the membrane spanning topology of LPAR6 helical segments. The present study further substantiated involvement of LPAR6-LPA signaling in the pathogenesis of hypotrichosis/woolly hair and provided additional insight into the molecular mechanism of hair development. PMID:25119526

  5. In Silico Analysis of Missense Mutations in LPAR6 Reveals Abnormal Phospholipid Signaling Pathway Leading to Hypotrichosis

    PubMed Central

    Raza, Syed Irfan; Muhammad, Dost; Jan, Abid; Ali, Raja Hussain; Hassan, Mubashir; Ahmad, Wasim; Rashid, Sajid

    2014-01-01

    Autosomal recessive hypotrichosis is a rare genetic irreversible hair loss disorder characterized by sparse scalp hair, sparse to absent eyebrows and eyelashes, and sparse axillary and body hair. The study, presented here, established genetic linkage in four families showing similar phenotypes to lysophosphatidic acid receptor 6 (LPAR6) gene on chromosome 13q14.11-q21.32. Subsequently, sequence analysis of the gene revealed two previously reported missense mutations including p.D63V in affected members of one and p.I188F in three other families. Molecular modeling and docking analysis was performed to investigate binding of a ligand oleoyl-L-alpha-lysophosphatidic acid (LPA) to modeled protein structures of normal and mutated (D63V, G146R, I188F, N248Y, S3T, L277P) LPAR6 receptors. The mutant receptors showed a complete shift in orientation of LPA at the binding site. In addition, hydropathy analysis revealed a significant change in the membrane spanning topology of LPAR6 helical segments. The present study further substantiated involvement of LPAR6-LPA signaling in the pathogenesis of hypotrichosis/woolly hair and provided additional insight into the molecular mechanism of hair development. PMID:25119526

  6. Revealing controllable nanowire transformation through cationic exchange for RRAM application.

    PubMed

    Huang, Chun-Wei; Chen, Jui-Yuan; Chiu, Chung-Hua; Wu, Wen-Wei

    2014-05-14

    One dimensional metal oxide nanostructures have attracted much attention owing to their fascinating functional properties. Among them, piezoelectricity and photocatalysts along with their related materials have stirred significant interests and widespread studies in recent years. In this work, we successfully transformed piezoelectric ZnO into photocatalytic TiO2 and formed TiO2/ZnO axial heterostructure nanowires with flat interfaces by solid to solid cationic exchange reactions in high vacuum (approximately 10(-8) Torr) transmission electron microscope (TEM). Kinetic behavior of the single crystalline TiO2 was systematically analyzed. The nanoscale growth rate of TiO2 has been measured using in situ TEM videos. On the basis of the rate, we can control the dimensions of the axial-nanoheterostructure. In addition, the unique Pt/ ZnO / TiO2/ ZnO /Pt heterostructures with complementary resistive switching (CRS) characteristics were designed to solve the important issue of sneak-peak current. The resistive switching behavior was attributed to the migration of oxygen and TiO2 layer served as reservoir, which was confirmed by energy dispersive spectrometry (EDS) analysis. This study not only supplied a distinct method to explore the transformation mechanisms but also exhibited the potential application of ZnO/TiO2 heterostructure in nanoscale crossbar array resistive random-access memory (RRAM). PMID:24742102

  7. Comparative genomics of oral isolates of Streptococcus mutans by in silico genome subtraction does not reveal accessory DNA associated with severe early childhood caries.

    PubMed

    Argimón, Silvia; Konganti, Kranti; Chen, Hao; Alekseyenko, Alexander V; Brown, Stuart; Caufield, Page W

    2014-01-01

    Comparative genomics is a popular method for the identification of microbial virulence determinants, especially since the sequencing of a large number of whole bacterial genomes from pathogenic and non-pathogenic strains has become relatively inexpensive. The bioinformatics pipelines for comparative genomics usually include gene prediction and annotation and can require significant computer power. To circumvent this, we developed a rapid method for genome-scale in silico subtractive hybridization, based on blastn and independent of feature identification and annotation. Whole genome comparisons by in silico genome subtraction were performed to identify genetic loci specific to Streptococcus mutans strains associated with severe early childhood caries (S-ECC), compared to strains isolated from caries-free (CF) children. The genome similarity of the 20 S. mutans strains included in this study, calculated by Simrank k-mer sharing, ranged from 79.5% to 90.9%, confirming this is a genetically heterogeneous group of strains. We identified strain-specific genetic elements in 19 strains, with sizes ranging from 200 to 39 kb. These elements contained protein-coding regions with functions mostly associated with mobile DNA. We did not, however, identify any genetic loci consistently associated with dental caries, i.e., shared by all the S-ECC strains and absent in the CF strains. Conversely, we did not identify any genetic loci specific with the healthy group. Comparison of previously published genomes from pathogenic and carriage strains of Neisseria meningitidis with our in silico genome subtraction yielded the same set of genes specific to the pathogenic strains, thus validating our method. Our results suggest that S. mutans strains derived from caries active or caries free dentitions cannot be differentiated based on the presence or absence of specific genetic elements. Our in silico genome subtraction method is available as the Microbial Genome Comparison (MGC) tool

  8. A comparative assessment of the transformation products of S-metolachlor and its commercial product Mercantor Gold(®) and their fate in the aquatic environment by employing a combination of experimental and in silico methods.

    PubMed

    Gutowski, Lukasz; Olsson, Oliver; Leder, Christoph; Kümmerer, Klaus

    2015-02-15

    Even appropriately used, pesticides can enter the surface and groundwater by several routes where photochemical degradation along with biotic processes contributes to their fate, resulting sometimes in the formation of stable transformation products (TPs). Yet, little is known about S-metolachlor (SM) transformation in the aquatic environment. Furthermore, commercial formulation of a pesticide might have different physical and biological properties compared to its pure grade. The present study assessed the biodegradability of the pure SM and its commercial product Mercantor Gold(®) (MG) by employing two OECD biodegradation (301D, F) tests. Photolysis in water was investigated by using a Xe lamp. Subsequently the biodegradability of the photolysis mixtures was examined. The primary elimination of SM was monitored and structures of its TPs were elucidated by HPLC-UV-MS/MS. Additionally, a set of in silico prediction programs was applied for supporting analytical results and toxicity assessment of SM and TPs. S-metolachlor and Mercantor Gold(®) were not biodegraded. HPLC-UV analysis showed higher elimination of SM in MG compared to pure SM during photolysis. A total of 10 photo-TPs of SM and MG were identified. According to MS data and in silico predictions, chemical structures were proposed for all found photo-TPs. Likewise for the parent compounds, no biodegradation has been observed for their photo-TPs. However, in the 301F test new bio-TPs have been generated from photo-TPs which were observed for the first time according to authors' best knowledge. The results suggest that the MG formulation does not affect the biodegradation process, but it influences the photolysis efficiency and potentially might result in faster formation of TPs in the environment. This study also demonstrates that photo-TPs can be further transformed into new products due to bacterial activity in the water phase. Moreover biotransformation might lead to an increased toxicity compared with

  9. In Silico and Fluorescence In Situ Hybridization Mapping Reveals Collinearity between the Pennisetum squamulatum Apomixis Carrier-Chromosome and Chromosome 2 of Sorghum and Foxtail Millet.

    PubMed

    Sapkota, Sirjan; Conner, Joann A; Hanna, Wayne W; Simon, Bindu; Fengler, Kevin; Deschamps, Stéphane; Cigan, Mark; Ozias-Akins, Peggy

    2016-01-01

    Apomixis, or clonal propagation through seed, is a trait identified within multiple species of the grass family (Poaceae). The genetic locus controlling apomixis in Pennisetum squamulatum (syn Cenchrus squamulatus) and Cenchrus ciliaris (syn Pennisetum ciliare, buffelgrass) is the apospory-specific genomic region (ASGR). Previously, the ASGR was shown to be highly conserved but inverted in marker order between P. squamulatum and C. ciliaris based on fluorescence in situ hybridization (FISH) and varied in both karyotype and position of the ASGR on the ASGR-carrier chromosome among other apomictic Cenchrus/Pennisetum species. Using in silico transcript mapping and verification of physical positions of some of the transcripts via FISH, we discovered that the ASGR-carrier chromosome from P. squamulatum is collinear with chromosome 2 of foxtail millet and sorghum outside of the ASGR. The in silico ordering of the ASGR-carrier chromosome markers, previously unmapped in P. squamulatum, allowed for the identification of a backcross line with structural changes to the P. squamulatum ASGR-carrier chromosome derived from gamma irradiated pollen. PMID:27031857

  10. In Silico and Fluorescence In Situ Hybridization Mapping Reveals Collinearity between the Pennisetum squamulatum Apomixis Carrier-Chromosome and Chromosome 2 of Sorghum and Foxtail Millet

    PubMed Central

    Sapkota, Sirjan; Conner, Joann A.; Hanna, Wayne W.; Simon, Bindu; Fengler, Kevin; Deschamps, Stéphane; Cigan, Mark; Ozias-Akins, Peggy

    2016-01-01

    Apomixis, or clonal propagation through seed, is a trait identified within multiple species of the grass family (Poaceae). The genetic locus controlling apomixis in Pennisetum squamulatum (syn Cenchrus squamulatus) and Cenchrus ciliaris (syn Pennisetum ciliare, buffelgrass) is the apospory-specific genomic region (ASGR). Previously, the ASGR was shown to be highly conserved but inverted in marker order between P. squamulatum and C. ciliaris based on fluorescence in situ hybridization (FISH) and varied in both karyotype and position of the ASGR on the ASGR-carrier chromosome among other apomictic Cenchrus/Pennisetum species. Using in silico transcript mapping and verification of physical positions of some of the transcripts via FISH, we discovered that the ASGR-carrier chromosome from P. squamulatum is collinear with chromosome 2 of foxtail millet and sorghum outside of the ASGR. The in silico ordering of the ASGR-carrier chromosome markers, previously unmapped in P. squamulatum, allowed for the identification of a backcross line with structural changes to the P. squamulatum ASGR-carrier chromosome derived from gamma irradiated pollen. PMID:27031857

  11. TRANSFORMATION

    SciTech Connect

    LACKS,S.A.

    2003-10-09

    Transformation, which alters the genetic makeup of an individual, is a concept that intrigues the human imagination. In Streptococcus pneumoniae such transformation was first demonstrated. Perhaps our fascination with genetics derived from our ancestors observing their own progeny, with its retention and assortment of parental traits, but such interest must have been accelerated after the dawn of agriculture. It was in pea plants that Gregor Mendel in the late 1800s examined inherited traits and found them to be determined by physical elements, or genes, passed from parents to progeny. In our day, the material basis of these genetic determinants was revealed to be DNA by the lowly bacteria, in particular, the pneumococcus. For this species, transformation by free DNA is a sexual process that enables cells to sport new combinations of genes and traits. Genetic transformation of the type found in S. pneumoniae occurs naturally in many species of bacteria (70), but, initially only a few other transformable species were found, namely, Haemophilus influenzae, Neisseria meningitides, Neisseria gonorrheae, and Bacillus subtilis (96). Natural transformation, which requires a set of genes evolved for the purpose, contrasts with artificial transformation, which is accomplished by shocking cells either electrically, as in electroporation, or by ionic and temperature shifts. Although such artificial treatments can introduce very small amounts of DNA into virtually any type of cell, the amounts introduced by natural transformation are a million-fold greater, and S. pneumoniae can take up as much as 10% of its cellular DNA content (40).

  12. Along Strike Heterogeneity of Seismic Slip Revealed by Oceanic Transform Fault Earthquakes

    NASA Astrophysics Data System (ADS)

    Aderhold, K.; Abercrombie, R. E.

    2015-12-01

    Oceanic transform faults (OTFs) are considered to have relatively simple structure [thermal, geometric, compositional], with the brittle-ductile transition defined by the 600-800ºC isotherm. Earthquakes on these faults account for less than half of the expected slip (Boettcher & Jordan, 2004), leaving the majority of motion to be accommodated aseismically. The 2015 MW7.1 Charlie-Gibbs transform earthquake is the latest of seven large [M≥6.25] earthquakes that form two quasi-repeating sequences dating back to 1920. These two sequences are separated by a region of persistent aseismicity in the center of the transform, interpreted to be a rupture barrier that prevents the full extent of the transform from rupturing in a single earthquake. However, aseismic rupture barriers alone cannot account for the inferred deficit in the seismic budget of OTFs. A growing catalogue of slip distributions has revealed distinctive behavior for large OTF earthquakes. We present evidence from teleseismic body wave modeling for directivity and slip distribution of four MW ≥ 7.0 oceanic strike-slip earthquakes: the 2015 MW7.1 Charlie-Gibbs transform earthquake in the North Atlantic, the 2015 MW7.0 Fourier transform earthquake in the South Atlantic, and the 2013 MW7.3 and 2006 MW7.4 South Sandwich transform earthquakes in the Southern Ocean. Each earthquake initiates near the ridge with nominal slip then propagates unilaterally to rupture larger asperities nearer the middle of the transform, similar to behavior observed for the 1994 MW7.0 Romanche transform earthquake. Significant continental strike-slip earthquakes, such as the 2002 MW7.9 Denali earthquake and the 2001 MW7.8 Kunlun earthquake, also exhibit unilateral ruptures with a small initial slip. The slip distributions of large oceanic transform earthquakes suggest that seismic coupling of OTFs varies considerably along strike, with large slip asperities separated by areas of little or no slip. Substantial earthquakes are not

  13. In Silico Analysis of the Genes Encoding Proteins that Are Involved in the Biosynthesis of the RMS/MAX/D Pathway Revealed New Roles of Strigolactones in Plants

    PubMed Central

    Marzec, Marek; Muszynska, Aleksandra

    2015-01-01

    Strigolactones were described as a new group of phytohormones in 2008 and since then notable large number of their functions has been uncovered, including the regulation of plant growth and development, interactions with other organisms and a plant’s response to different abiotic stresses. In the last year, investigations of the strigolactone biosynthesis pathway in two model species, Arabidopsis thaliana and Oryza sativa, resulted in great progress in understanding the functions of four enzymes that are involved in this process. We performed in silico analyses, including the identification of the cis-regulatory elements in the promoters of genes encoding proteins of the strigolactone biosynthesis pathway and the identification of the miRNAs that are able to regulate their posttranscriptional level. We also searched the databases that contain the microarray data for the genes that were analyzed from both species in order to check their expression level under different growth conditions. The results that were obtained indicate that there are universal regulations of expression of all of the genes that are involved in the strigolactone biosynthesis in Arabidopsis and rice, but on the other hand each stage of strigolactone production may be additionally regulated independently. This work indicates the presence of crosstalk between strigolactones and almost all of the other phytohormones and suggests the role of strigolactones in the response to abiotic stresses, such as wounding, cold or flooding, as well as in the response to biotic stresses. PMID:25815594

  14. Initial hazard screening for genotoxicity of photo-transformation products of ciprofloxacin by applying a combination of experimental and in-silico testing.

    PubMed

    Toolaram, Anju Priya; Haddad, Tarek; Leder, Christoph; Kümmerer, Klaus

    2016-04-01

    Ciprofloxacin (CIP) is a broad-spectrum antibiotic found within μg/L concentration range in the aquatic environment. It is a known contributor of umuC induction in hospital wastewater samples. CIP can undergo photolysis to result in many transformation products (TPs) of mostly unknown toxicity. The aims of this study were to determine the genotoxicity of the UV mixtures and to understand the possible genotoxic role of the stable TPs. As such, CIP and its UV-irradiated mixtures were investigated in a battery of genotoxicity and cytotoxicity in vitro assays. The combination index (CI) analysis of residual CIP in the irradiated mixtures was performed for the umu assay. Further, Quantitative Structure-Activity Relationships (QSARs) predicted selected genotoxicity endpoints of the identified TPs. CIP achieved primary elimination after 128 min of irradiation but was not completely mineralized. Nine photo-TPs were identified. The irradiated mixtures were neither mutagenic in the Ames test nor genotoxic in the in vitro micronucleus (MN) test. Like CIP, the irradiated mixtures were umuC inducing. The CI analysis revealed that the irradiated mixtures and the corresponding CIP concentration in the mixtures shared similar umuC potentials. QSAR predictions suggested that the TPs may be capable of inducing chromosome aberration, MN in vivo, bacterial mutation and mammalian mutation. However, the experimental testing for a few genotoxic endpoints did not show significant genotoxic activity for the TPs present as a component of the whole mixture analysis and therefore, further genotoxic endpoints may need to be investigated to fully confirm this. PMID:26748250

  15. V-region mutation in vitro, in vivo, and in silico reveal the importance of the enzymatic properties of AID and the sequence environment

    PubMed Central

    MacCarthy, Thomas; Kalis, Susan L.; Roa, Sergio; Pham, Phuong; Goodman, Myron F.; Scharff, Matthew D.; Bergman, Aviv

    2009-01-01

    The somatic hypermutation of Ig variable regions requires the activity of activation-induced cytidine deaminase (AID) which has previously been shown to preferentially deaminate WRC (W = A/T, R = A/G) motif hot spots in in vivo and in vitro assays. We compared mutation profiles of in vitro assays for the 3′ flanking intron of VhJ558-Jh4 region to previously reported in vivo profiles for the same region in the Msh2−/−Ung−/− mice that lack base excision and mismatch repair. We found that the in vitro and in vivo mutation profiles were highly correlated for the top (nontranscribed) strand, while for the bottom (transcribed) strand the correlation is far lower. We used an in silico model of AID activity to elucidate the relative importance of motif targeting in vivo. We found that the mutation process entails substantial complexity beyond motif targeting, a large part of which is captured in vitro. To elucidate the contribution of the sequence environment to the observed differences between the top and bottom strands, we analyzed intermutational distances. The bottom strand shows an approximately exponential distribution of distances in vivo and in vitro, as expected from a null model. However, the top strand deviates strongly from this distribution in that mutations approximately 50 nucleotides apart are greatly reduced, again both in vivo and in vitro, illustrating an important strand asymmetry. While we have confirmed that AID targeting of hot and cold spots is a key part of the mutation process, our results suggest that the sequence environment plays an equally important role. PMID:19443686

  16. In silico Analysis of HIV-1 Env-gp120 Reveals Structural Bases for Viral Adaptation in Growth-Restrictive Cells

    PubMed Central

    Yokoyama, Masaru; Nomaguchi, Masako; Doi, Naoya; Kanda, Tadahito; Adachi, Akio; Sato, Hironori

    2016-01-01

    Variable V1/V2 and V3 loops on human immunodeficiency virus type 1 (HIV-1) envelope-gp120 core play key roles in modulating viral competence to recognize two infection receptors, CD4 and chemokine-receptors. However, molecular bases for the modulation largely remain unclear. To address these issues, we constructed structural models for a full-length gp120 in CD4-free and -bound states. The models showed topologies of gp120 surface loop that agree with those in reported structural data. Molecular dynamics simulation showed that in the unliganded state, V1/V2 loop settled into a thermodynamically stable arrangement near V3 loop for conformational masking of V3 tip, a potent neutralization epitope. In the CD4-bound state, however, V1/V2 loop was rearranged near the bound CD4 to support CD4 binding. In parallel, cell-based adaptation in the absence of anti-viral antibody pressures led to the identification of amino acid substitutions that individually enhance viral entry and growth efficiencies in association with reduced sensitivity to CCR5 antagonist TAK-779. Notably, all these substitutions were positioned on the receptors binding surfaces in V1/V2 or V3 loop. In silico structural studies predicted some physical changes of gp120 by substitutions with alterations in viral replication phenotypes. These data suggest that V1/V2 loop is critical for creating a gp120 structure that masks co-receptor binding site compatible with maintenance of viral infectivity, and for tuning a functional balance of gp120 between immune escape ability and infectivity to optimize HIV-1 replication fitness. PMID:26903989

  17. In silico Analysis Revealed High-risk Single Nucleotide Polymorphisms in Human Pentraxin-3 Gene and their Impact on Innate Immune Response against Microbial Pathogens

    PubMed Central

    Thakur, Raman; Shankar, Jata

    2016-01-01

    Pentraxin-3 (PTX-3) protein is an evolutionary conserved protein that acts as a soluble pattern-recognition receptor for pathogens and plays important role in innate immune response. It recognizes various pathogens by interacting with extracellular moieties such as glactomannan of conidia (Aspergillus fumigatus), lipopolysaccharide of Pseudomonas aeruginosa, Streptococcus pneumonia and Salmonella typhimurium. Thus, PTX-3 protein helps to clear these pathogens by activating downstream innate immune process. In this study, computational methods were used to analyze various non-synonymous single nucleotide polymorphisms (nsSNPs) in PTX-3 gene. Three different databases were used to retrieve SNP data sets followed by seven different in silico algorithms to screen nsSNPs in PTX-3 gene. Sequence homology based approach was used to identify nsSNPs. Conservation profile of PTX-3 protein amino acid residues were predicted by ConSurf web server. In total, 10 high-risk nsSNPs were identified in pentraxin-domain of PTX-3 gene. Out of these 10 high-risk nsSNPs, 4 were present in the conserved structural and functional residues of the pentraxin-domain, hence, selected for structural analyses. The results showed alteration in the putative structure of pentraxin-domain. Prediction of protein–protein interactions analysis showed association of PTX-3 protein with C1q component of complement pathway. Different functional and structural residues along with various putative phosphorylation sites and evolutionary relationship were also predicted for PTX-3 protein. This is the first extensive computational analyses of pentraxin protein family with nsSNPs and will serve as a valuable resource for future population based studies. PMID:26941719

  18. In Silico Screening for Palmitoyl Substrates Reveals a Role for DHHC1/3/10 (zDHHC1/3/11)-mediated Neurochondrin Palmitoylation in Its Targeting to Rab5-positive Endosomes*

    PubMed Central

    Oku, Shinichiro; Takahashi, Naoki; Fukata, Yuko; Fukata, Masaki

    2013-01-01

    Protein palmitoylation, a common post-translational lipid modification, plays an important role in protein trafficking and functions. Recently developed palmitoyl-proteomic methods identified many novel substrates. However, the whole picture of palmitoyl substrates has not been clarified. Here, we performed global in silico screening using the CSS-Palm 2.0 program, free software for prediction of palmitoylation sites, and selected 17 candidates as novel palmitoyl substrates. Of the 17 candidates, 10 proteins, including 6 synaptic proteins (Syd-1, transmembrane AMPA receptor regulatory protein (TARP) γ-2, TARP γ-8, cornichon-2, Ca2+/calmodulin-dependent protein kinase IIα, and neurochondrin (Ncdn)/norbin), one focal adhesion protein (zyxin), two ion channels (TRPM8 and TRPC1), and one G-protein-coupled receptor (orexin 2 receptor), were palmitoylated. Using the DHHC palmitoylating enzyme library, we found that all tested substrates were palmitoylated by the Golgi-localized DHHC3/7 subfamily. Ncdn, a regulator for neurite outgrowth and synaptic plasticity, was robustly palmitoylated by the DHHC1/10 (zDHHC1/11; z1/11) subfamily, whose substrate has not yet been reported. As predicted by CSS-Palm 2.0, Cys-3 and Cys-4 are the palmitoylation sites for Ncdn. Ncdn was specifically localized in somato-dendritic regions, not in the axon of rat cultured neurons. Stimulated emission depletion microscopy revealed that Ncdn was localized to Rab5-positive early endosomes in a palmitoylation-dependent manner, where DHHC1/10 (z1/11) were also distributed. Knockdown of DHHC1, -3, or -10 (z11) resulted in the loss of Ncdn from Rab5-positive endosomes. Thus, through in silico screening, we demonstrate that Ncdn and the DHHC1/10 (z1/11) and DHHC3/7 subfamilies are novel palmitoyl substrate-enzyme pairs and that Ncdn palmitoylation plays an essential role in its specific endosomal targeting. PMID:23687301

  19. The Early ULF Signal of the Gigantic Jets Revealed By Hilbert-Huang Transform

    NASA Astrophysics Data System (ADS)

    Huang, Po-Hsun; Bing-Chih Chen, Alfred

    2015-04-01

    The conventional Fourier analysis on the sferics in ULF and VLF bandpasses has been done for years. Several phenomena e.g. whistler and Schumann resonance have been well studied by the Fourier spectrum comprehensively. But the Fourier analysis is computed by an integration over time, therefore, the temporal resolution is smoothed, and limited not only by the sampling rate but also the size of the integration window. The instantaneous frequency can't be obtained through this conventional approach. We introduce the Hilbert-Huang transform (HHT) instead of Fourier transform to analyze the sferics of TLEs recorded at Lulin observatory. The Hilbert-Huang transform decomposes a signal into so-called intrinsic mode functions (IMF), and derive instantaneous frequency data by differentiating the phase angle yielded by Hilbert transform. Our analysis of HHT on several gigantic jets recorded by ground observation surprisingly revealed an early signal of frequency-change during the phase of the leading jet, and this early signal can not be identified by Fourier analysis. In the phase of leading jet, the amplitude of the sferics remains a constant and no significant features are recognized in the recorded waveform, but an obvious frequency change about 100-200 millisecond prior to the main discharge of the full development jets (FDJs), which can be clearly recognized in the HHT spectra of all observed gigantic jets. From a further simulation, this frequency change is confirmed to come from the nature of the discharge, not an alias or a false signal generated by the analysis method. This early signal may implies an in-cloud discharge process which is suggested by Krehbiel et al. [2008

  20. In Silico Expression Analysis.

    PubMed

    Bolívar, Julio; Hehl, Reinhard; Bülow, Lorenz

    2016-01-01

    Information on the specificity of cis-sequences enables the design of functional synthetic plant promoters that are responsive to specific stresses. Potential cis-sequences may be experimentally tested, however, correlation of genomic sequence with gene expression data enables an in silico expression analysis approach to bioinformatically assess the stress specificity of candidate cis-sequences prior to experimental verification. The present chapter demonstrates an example for the in silico validation of a potential cis-regulatory sequence responsive to cold stress. The described online tool can be applied for the bioinformatic assessment of cis-sequences responsive to most abiotic and biotic stresses of plants. Furthermore, a method is presented based on a reverted in silico expression analysis approach that predicts highly specific potentially functional cis-regulatory elements for a given stress. PMID:27557772

  1. Interspecific Comparison of the Transformer Gene of Drosophila Reveals an Unusually High Degree of Evolutionary Divergence

    PubMed Central

    O'Neil, M. T.; Belote, J. M.

    1992-01-01

    The transformer (tra) gene of Drosophila melanogaster occupies an intermediate position in the regulatory pathway controlling all aspects of somatic sexual differentiation. The female-specific expression of this gene's function is regulated by the Sex lethal (Sxl) gene, through a mechanism involving sex-specific alternative splicing of tra pre-mRNA. The tra gene encodes a protein that is thought to act in conjunction with the transformer-2 (tra-2) gene product to control the sex-specific processing of doublesex (dsx) pre-mRNA. The bifunctional dsx gene carries out opposite functions in the two sexes, repressing female differentiation in males and repressing male differentiation in females. Here we report the results from an evolutionary approach to investigate tra regulation and function, by isolating the tra-homologous genes from selected Drosophila species, and then using the interpecific DNA sequence comparisons to help identify regions of functional significance. The tra-homologous genes from two Sophophoran subgenus species, Drosophila simulans and Drosophila erecta, and two Drosophila subgenus species, Drosophila hydei and Drosophila virilis, were cloned, sequenced and compared to the D. melanogaster tra gene. This comparison reveals an unusually high degree of evolutionary divergence among the tra coding sequences. These studies also highlight a highly conserved sequence within intron one that probably defines a cis-acting regulator of the sex-specific alternative splicing event. PMID:1592233

  2. Bovine α₁-acid glycoprotein, a thermostable version of its human counterpart: insights from Fourier transform infrared spectroscopy and in silico modelling.

    PubMed

    Baldassarre, Maurizio; Galeazzi, Roberta; Maggiore, Beatrice; Tanfani, Fabio; Scirè, Andrea

    2014-07-01

    α1-Acid glycoprotein (AGP) is a plasma protein and a member of the acute phase response. AGP is known to bind and carry several biologically active compounds, as well as to down-modulate the immune system activities. In this work, the structure of bovine AGP has been investigated by Fourier-Transform infrared spectroscopy. A model structure has been obtained on the basis of human AGP and refined by molecular dynamics. In spite of the similar structure, bovine AGP shows an unexpectedly higher (∼20 °C) thermostability than its human counterpart. Inspection of the model structure has pointed out the presence of 12 ionic bridges and 2 sulphur-aromatic interactions, whereas only 6 ionic bridges were detected in human AGP. The high number (9) of glutamic acid residues involved in the ionic interactions might explain the significantly decreased thermostability measured at pH 5.5 (Tm ∼ 71 °C) with respect to pH 7.4 (Tm ∼ 81 °C), whereas thermostability of human AGP was only slightly affected by lowering the pH. As in human AGP and several other lipocalins, a temperature-induced molten globule state has been observed in the denaturation pathway of bovine AGP. PMID:24530968

  3. Molecular structure of tetanus neurotoxin as revealed by Fourier transform infrared and circular dichroic spectroscopy.

    PubMed

    Singh, B R; Fuller, M P; Schiavo, G

    1990-07-01

    Secondary structure contents of tetanus neurotoxin have been estimated at neutral and acidic pH using circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy. An analysis of the far-ultraviolet CD spectra of the neurotoxin dissolved in 50 mM citrate-phosphate buffer (pH 7.0) revealed 20.0 +/- 2.1% alpha-helix, 50.5 +/- 2.1% beta-pleated sheets, no beta-turns, and 29.5% random coils, which is at considerable variance with results from an earlier detailed study of tetanus neurotoxin's secondary structures (J.P. Robinson, L.A. Holladay, J.H. Hash and D. Puett, J. Biol. Chem. 257 (1982) 407). However, the alpha-helix content estimated in this study is consistent with the earlier studies of Robinson et al. (J.P. Robinson, L.A. Holladay, J.B. Picklesimer and D. Puett, Mol. Cell. Biochem. 5 (1974) 147; J.P. Robinson, J.B. Picklesimer and D. Puett, J. Biol. Chem. 250 (1975) 7435) and with the study by Lazarovici et al. (P. Lazarovici, P. Yanai and E. Yavin, J. Biol. Chem. 262 (1986) 2645), although other secondary structural features do not agree with those of the previous studies. Secondary structure estimation from Fourier transform infrared spectra in both amide I and amide III frequency regions revealed 22-23% alpha-helix, 49-51% beta-pleated sheets and 27-28% random coils, indicating a good correlation with the secondary structure content estimated from CD analysis. Lowering of the pH of the neurotoxin to 5.5 or 4.0 did not result in any noticeable change in the overall secondary structures. However, there were significant pH-induced variations observed in the individual curve-fitted FT-IR bands in the amide III frequency region. For example, the 1302 cm-1 band (relative area, 4.2%) observed at pH 7.0 was shifted to 1297 cm-1 (relative area, 2.2%) at pH 5.5, and the relative area of the band at 1316-1317 cm-1 (alpha-helix) increased by approx. 40%. This study suggests that contrary to earlier reports, tetanus neurotoxin is a beta-pleated sheet

  4. The Complexity of Posttranscriptional Small RNA Regulatory Networks Revealed by In Silico Analysis of Gossypium arboreum L. Leaf, Flower and Boll Small Regulatory RNAs

    PubMed Central

    Hu, Hongtao; Rashotte, Aaron M.; Singh, Narendra K.; Weaver, David B.; Goertzen, Leslie R.; Singh, Shree R.; Locy, Robert D.

    2015-01-01

    MicroRNAs (miRNAs) and secondary small interfering RNAs (principally phased siRNAs or trans-acting siRNAs) are two distinct subfamilies of small RNAs (sRNAs) that are emerging as key regulators of posttranscriptional gene expression in plants. Both miRNAs and secondary-siRNAs (sec-siRNAs) are processed from longer RNA precursors by DICER-LIKE proteins (DCLs). Gossypium arboreum L., also known as tree cotton or Asian cotton, is a diploid, possibly ancestral relative of tetraploid Gossypium hirsutum L., the predominant type of commercially grown cotton worldwide known as upland cotton. To understand the biological significance of these gene regulators in G. arboreum, a bioinformatics analysis was performed on G. arboreum small RNAs produced from G. arboreum leaf, flower, and boll tissues. Consequently, 263 miRNAs derived from 353 precursors, including 155 conserved miRNAs (cs-miRNAs) and 108 novel lineage-specific miRNAs (ls-miRNAs). Along with miRNAs, 2,033 miRNA variants (isomiRNAs) were identified as well. Those isomiRNAs with variation at the 3’-miRNA end were expressed at the highest levels, compared to other types of variants. In addition, 755 pha-siRNAs derived 319 pha-siRNA gene transcripts (PGTs) were identified, and the potential pha-siRNA initiators were predicted. Also, 2,251 non-phased siRNAs were found as well, of which 1,088 appeared to be produced by so-called cis- or trans-cleavage of the PGTs observed at positions differing from pha-siRNAs. Of those sRNAs, 148 miRNAs/isomiRNAs and 274 phased/non-phased siRNAs were differentially expressed in one or more pairs of tissues examined. Target analysis revealed that target genes for both miRNAs and pha-siRNAs are involved a broad range of metabolic and enzymatic activities. We demonstrate that secondary siRNA production could result from initial cleavage of precursors by both miRNAs or isomiRNAs, and that subsequently produced phased and unphased siRNAs could result that also serve as triggers of a

  5. TRANSFORMER

    DOEpatents

    Baker, W.R.

    1959-08-25

    Transformers of a type adapted for use with extreme high power vacuum tubes where current requirements may be of the order of 2,000 to 200,000 amperes are described. The transformer casing has the form of a re-entrant section being extended through an opening in one end of the cylinder to form a coaxial terminal arrangement. A toroidal multi-turn primary winding is disposed within the casing in coaxial relationship therein. In a second embodiment, means are provided for forming the casing as a multi-turn secondary. The transformer is characterized by minimized resistance heating, minimized external magnetic flux, and an economical construction.

  6. Microchemical Structure of Soybean Seeds Revealed in Situ by Ultraspatially Resolved Synchrotron Fourier Transformed Infrared Microspectroscopy

    SciTech Connect

    Pietrzak,L.; Miller, S.

    2005-01-01

    The distribution of water in soybean seeds during imbibition varies with the chemical composition of the tissue. To understand the dynamics of imbibition, the proteins, lipids, and carbohydrates of the cotyledons and hilum region in mature soybean seeds were mapped using synchrotron Fourier transformed infrared microspectroscopy, based on characteristic peaks for each component: amide I at 1650 cm{sup -1} and amide II at 1550 cm{sup -1} for protein, lipid ester stretch at 1545 cm{sup -1}, and the region from 1200 to 900 cm{sup -1} for carbohydrates. The amount and configuration of the proteins varied across the cotyledon, as well as the amount of lipid and carbohydrate. It was found that protein distribution across the cotyledon is similar to water distribution during imbibition. The chemistry of the hilum region was also studied, as this is the point of water entry, and differences in the chemical composition of the tissues studied were observed.

  7. Poking vesicles in silico

    NASA Astrophysics Data System (ADS)

    Barlow, Ben; Bertrand, Martin; Joos, Bela

    2014-03-01

    The Atomic Force Microscope (AFM) is used to poke cells and study their mechanical properties. Using Coarse-Grained Molecular Dynamics simulations, we study the deformation and relaxation of lipid bilayer vesicles, when poked with a constant force. The relaxation time, equilibrium area expansion, and surface tension of the vesicle membrane are studied over a range of applied forces. The relaxation time exhibits a strong force-dependence. Our force-compression curves show a strong similarity with results from a recent experiment by Schafer et al. (Langmuir, 2013). They used an AFM to ``poke'' adherent giant liposomes with constant nanonewton forces and observed the resulting deformation with a Laser Scanning Confocal Microscope. Results of such experiments, whether on vesicles or cells, are often interpreted in terms of dashpots and springs. This simple approach used to describe the response of a whole cell --complete with cytoskeleton, organelles etc.-- can be problematic when trying to measure the contribution of a single cell component. Our modeling is a first step in a ``bottom-up'' approach where we investigate the viscoelastic properties of an in silico cell prototype with constituents added step by step. Supported by NSERC (Canada).

  8. Clonal Evolution Revealed by Whole Genome Sequencing in a Case of Primary Myelofibrosis Transformed to Secondary Acute Myeloid Leukemia

    PubMed Central

    Engle, Elizabeth K.; Fisher, Daniel A.C.; Miller, Christopher A.; McLellan, Michael D.; Fulton, Robert S.; Moore, Deborah M.; Wilson, Richard K.; Ley, Timothy J.; Oh, Stephen T.

    2014-01-01

    Clonal architecture in myeloproliferative neoplasms (MPNs) is poorly understood. Here we report genomic analyses of a patient with primary myelofibrosis (PMF) transformed to secondary acute myeloid leukemia (sAML). Whole genome sequencing (WGS) was performed on PMF and sAML diagnosis samples, with skin included as a germline surrogate. Deep sequencing validation was performed on the WGS samples and an additional sample obtained during sAML remission/relapsed PMF. Clustering analysis of 649 validated somatic single nucleotide variants revealed four distinct clonal groups, each including putative driver mutations. The first group (including JAK2 and U2AF1), representing the founding clone, included mutations with high frequency at all three disease stages. The second clonal group (including MYB) was present only in PMF, suggesting the presence of a clone that was dispensable for transformation. The third group (including ASXL1) contained mutations with low frequency in PMF and high frequency in subsequent samples, indicating evolution of the dominant clone with disease progression. The fourth clonal group (including IDH1 and RUNX1) was acquired at sAML transformation and was predominantly absent at sAML remission/relapsed PMF. Taken together, these findings illustrate the complex clonal dynamics associated with disease evolution in MPNs and sAML. PMID:25252869

  9. A Quantitative Toxicogenomics Assay Reveals the Evolution and Nature of Toxicity during the Transformation of Environmental Pollutants

    PubMed Central

    2015-01-01

    The incomplete mineralization of contaminants of emerging concern (CECs) during the advanced oxidation processes can generate transformation products that exhibit toxicity comparable to or greater than that of the original contaminant. In this study, we demonstrated the application of a novel, fast, and cost-effective quantitative toxicogenomics-based approach for the evaluation of the evolution and nature of toxicity along the electro-Fenton oxidative degradation of three representative CECs whose oxidative degradation pathways have been relatively well studied, bisphenol A, triclosan, and ibuprofen. The evolution of toxicity as a result of the transformation of parent chemicals and production of intermediates during the course of degradation are monitored, and the quantitative toxicogenomics assay results revealed the dynamic toxicity changes and mechanisms, as well as their association with identified intermediates during the electro-Fenton oxidation process of the selected CECs. Although for the three CECs, a majority (>75%) of the parent compounds disappeared at the 15 min reaction time, the nearly complete elimination of toxicity required a minimal 30 min reaction time, and they seem to correspond to the disappearance of identified aromatic intermediates. Bisphenol A led to a wide range of stress responses, and some identified transformation products containing phenolic or quinone group, such as 1,4-benzoquinone and hydroquinone, likely contributed to the transit toxicity exhibited as DNA stress (genotoxicity) and membrane stress during the degradation. Triclosan is known to cause severe oxidative stress, and although the oxidative damage potential decreased concomitantly with the disappearance of triclosan after a 15 min reaction, the sustained toxicity associated with both membrane and protein stress was likely attributed at least partially to the production of 2,4-dichlorophenol that is known to cause the production of abnormal proteins and affect the cell

  10. A quantitative toxicogenomics assay reveals the evolution and nature of toxicity during the transformation of environmental pollutants.

    PubMed

    Gou, Na; Yuan, Songhu; Lan, Jiaqi; Gao, Ce; Alshawabkeh, Akram N; Gu, April Z

    2014-01-01

    The incomplete mineralization of contaminants of emerging concern (CECs) during the advanced oxidation processes can generate transformation products that exhibit toxicity comparable to or greater than that of the original contaminant. In this study, we demonstrated the application of a novel, fast, and cost-effective quantitative toxicogenomics-based approach for the evaluation of the evolution and nature of toxicity along the electro-Fenton oxidative degradation of three representative CECs whose oxidative degradation pathways have been relatively well studied, bisphenol A, triclosan, and ibuprofen. The evolution of toxicity as a result of the transformation of parent chemicals and production of intermediates during the course of degradation are monitored, and the quantitative toxicogenomics assay results revealed the dynamic toxicity changes and mechanisms, as well as their association with identified intermediates during the electro-Fenton oxidation process of the selected CECs. Although for the three CECs, a majority (>75%) of the parent compounds disappeared at the 15 min reaction time, the nearly complete elimination of toxicity required a minimal 30 min reaction time, and they seem to correspond to the disappearance of identified aromatic intermediates. Bisphenol A led to a wide range of stress responses, and some identified transformation products containing phenolic or quinone group, such as 1,4-benzoquinone and hydroquinone, likely contributed to the transit toxicity exhibited as DNA stress (genotoxicity) and membrane stress during the degradation. Triclosan is known to cause severe oxidative stress, and although the oxidative damage potential decreased concomitantly with the disappearance of triclosan after a 15 min reaction, the sustained toxicity associated with both membrane and protein stress was likely attributed at least partially to the production of 2,4-dichlorophenol that is known to cause the production of abnormal proteins and affect the cell

  11. Evolving phenotypic networks in silico.

    PubMed

    François, Paul

    2014-11-01

    Evolved gene networks are constrained by natural selection. Their structures and functions are consequently far from being random, as exemplified by the multiple instances of parallel/convergent evolution. One can thus ask if features of actual gene networks can be recovered from evolutionary first principles. I review a method for in silico evolution of small models of gene networks aiming at performing predefined biological functions. I summarize the current implementation of the algorithm, insisting on the construction of a proper "fitness" function. I illustrate the approach on three examples: biochemical adaptation, ligand discrimination and vertebrate segmentation (somitogenesis). While the structure of the evolved networks is variable, dynamics of our evolved networks are usually constrained and present many similar features to actual gene networks, including properties that were not explicitly selected for. In silico evolution can thus be used to predict biological behaviours without a detailed knowledge of the mapping between genotype and phenotype. PMID:24956562

  12. Cardiac mechanoenergetics in silico.

    PubMed

    Vendelin, Marko; Bovendeerd, Peter H M; Saks, Valdur; Engelbrecht, Jüri

    2002-02-01

    The aim of this thesis is to investigate the link between biochemical intracellular processes and mechanical contraction of the cardiac muscle. First, the regulation of intracellular energy fluxes between mitochondria and myofibrils is studied. It is shown, that the experimentally observed metabolic stability of the cardiac muscle is reproducible by a simple feedback regulation mechanism, i.e., ATP consumption in myofibrils and ATP production in mitochondria are balanced by the changes of the high energy phosphate concentrations. Second, an important property of energy transformation from biochemical form to mechanical work in the cardiac muscle, the linear relationship between the oxygen consumption and the stress-strain area, is replicated by a cross-bridge model. Third, by using the developed cross-bridge model, the correlation between ejection fraction of the left ventricle and heterogeneity of sarcomere strain, developed stress and ATP consumption in the left ventricular wall is established. Fourth, an experimentally observed linear relationship between oxygen consumption and the pressure-volume area can be predicted theoretically from a linear relationship between the oxygen consumption and the stress-strain area. Summing up, it is shown how the macrovariables of a cardiac muscle are interwoven with intracellular physiological processes into a whole. PMID:11880857

  13. Surface plasmon resonance imaging reveals multiple binding modes of Agrobacterium transformation mediator VirE2 to ssDNA

    PubMed Central

    Kim, Sanghyun; Zbaida, David; Elbaum, Michael; Leh, Hervé; Nogues, Claude; Buckle, Malcolm

    2015-01-01

    VirE2 is the major secreted protein of Agrobacterium tumefaciens in its genetic transformation of plant hosts. It is co-expressed with a small acidic chaperone VirE1, which prevents VirE2 oligomerization. After secretion into the host cell, VirE2 serves functions similar to a viral capsid in protecting the single-stranded transferred DNA en route to the nucleus. Binding of VirE2 to ssDNA is strongly cooperative and depends moreover on protein–protein interactions. In order to isolate the protein–DNA interactions, imaging surface plasmon resonance (SPRi) studies were conducted using surface-immobilized DNA substrates of length comparable to the protein-binding footprint. Binding curves revealed an important influence of substrate rigidity with a notable preference for poly-T sequences and absence of binding to both poly-A and double-stranded DNA fragments. Dissociation at high salt concentration confirmed the electrostatic nature of the interaction. VirE1–VirE2 heterodimers also bound to ssDNA, though by a different mechanism that was insensitive to high salt. Neither VirE2 nor VirE1–VirE2 followed the Langmuir isotherm expected for reversible monomeric binding. The differences reflect the cooperative self-interactions of VirE2 that are suppressed by VirE1. PMID:26044711

  14. In Silico Experimental Modeling of Cancer Treatment

    PubMed Central

    Trisilowati; Mallet, D. G.

    2012-01-01

    In silico experimental modeling of cancer involves combining findings from biological literature with computer-based models of biological systems in order to conduct investigations of hypotheses entirely in the computer laboratory. In this paper, we discuss the use of in silico modeling as a precursor to traditional clinical and laboratory research, allowing researchers to refine their experimental programs with an aim to reducing costs and increasing research efficiency. We explain the methodology of in silico experimental trials before providing an example of in silico modeling from the biomathematical literature with a view to promoting more widespread use and understanding of this research strategy. PMID:22523709

  15. Component analysis and growth process of nasopharyngeal calculus as revealed by Fourier transform infrared (FT-IR) spectroscopy.

    PubMed

    Ogawa, T; Shibata, A; Maeda, Y; Uno, Y; Okano, M; Nishizaki, K; Ohsaki, K

    2003-06-01

    A quite rare case of nasopharyngeal calculus in a woman in her twenties associated with the nasal discharge of pseudomonas infection was reported. As the substance was irregularly large in size, we extracted it partially by piecemeal resection using forceps and also by cracking technique using the holmium yttrium-aluminum-garnet (YAG) laser, under saline irrigation and stereotactic microscopic navigator (SMN) system under endoscopic observation. The substance was firmly fixed to the pharyngeal tonsil bed. The final extract was a small piece of singly folded bandage, which is probably the focal background for calculus formation. In a cross section of calculus specimen removed during surgery, Fourier transform infrared (FT-IR) analysis revealed that a) signal ratio of methylene group (organic substance) to amide I (protein) was 21.6% at the nasal cavity side, gradually decreased toward nasal mucous membrane showing approximate 50%, b) signal ratio of amide I to P04(3-) (inorganic substance) ranged between 17.7% and 26.7% at the different sites and inside the calculus, the protein content was approximate 1/5 of the inorganic substance, and c) signal ratio of the methylene group to amide I at the nasal cavity site showed that their contents were almost equal. The quantity of the organic substance was estimated at approximate 1/2 quantity of the protein at both the central part and the part contacted with the mucous membrane. From these results, it seems that throughout the course of calculus growth, both inorganic substance and protein remain almost constant inside the calculus, while organic substance is released from the internal part of the calculus being probably formed at an early stage. PMID:12899453

  16. Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium

    PubMed Central

    Barbe, Valérie; Vallenet, David; Fonknechten, Nuria; Kreimeyer, Annett; Oztas, Sophie; Labarre, Laurent; Cruveiller, Stéphane; Robert, Catherine; Duprat, Simone; Wincker, Patrick; Ornston, L. Nicholas; Weissenbach, Jean; Marlière, Philippe; Cohen, Georges N.; Médigue, Claudine

    2004-01-01

    Acinetobacter sp. strain ADP1 is a nutritionally versatile soil bacterium closely related to representatives of the well-characterized Pseudomonas aeruginosa and Pseudomonas putida. Unlike these bacteria, the Acinetobacter ADP1 is highly competent for natural transformation which affords extraordinary convenience for genetic manipulation. The circular chromosome of the Acinetobacter ADP1, presented here, encodes 3325 predicted coding sequences, of which 60% have been classified based on sequence similarity to other documented proteins. The close evolutionary proximity of Acinetobacter and Pseudomonas species, as judged by the sequences of their 16S RNA genes and by the highest level of bidirectional best hits, contrasts with the extensive divergence in the GC content of their DNA (40 versus 62%). The chromosomes also differ significantly in size, with the Acinetobacter ADP1 chromosome <60% of the length of the Pseudomonas counterparts. Genome analysis of the Acinetobacter ADP1 revealed genes for metabolic pathways involved in utilization of a large variety of compounds. Almost all of these genes, with orthologs that are scattered in other species, are located in five major ‘islands of catabolic diversity’, now an apparent ‘archipelago of catabolic diversity’, within one-quarter of the overall genome. Acinetobacter ADP1 displays many features of other aerobic soil bacteria with metabolism oriented toward the degradation of organic compounds found in their natural habitat. A distinguishing feature of this genome is the absence of a gene corresponding to pyruvate kinase, the enzyme that generally catalyzes the terminal step in conversion of carbohydrates to pyruvate for respiration by the citric acid cycle. This finding supports the view that the cycle itself is centrally geared to the catabolic capabilities of this exceptionally versatile organism. PMID:15514110

  17. Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology

    PubMed Central

    Milne, Caroline B.; Kim, Pan-Jun; Eddy, James A.; Price, Nathan D.

    2011-01-01

    Driven by advancements in high-throughput biological technologies and the growing number of sequenced genomes, the construction of in silico models at the genome scale has provided powerful tools to investigate a vast array of biological systems and applications. Here, we review comprehensively the uses of such models in industrial and medical biotechnology, including biofuel generation, food production, and drug development. While the use of in silico models is still in its early stages for delivering to industry, significant initial successes have been achieved. For the cases presented here, genome-scale models predict engineering strategies to enhance properties of interest in an organism or to inhibit harmful mechanisms of pathogens or in disease. Going forward, genome-scale in silico models promise to extend their application and analysis scope to become a transformative tool in biotechnology. As such, genome-scale models can provide a basis for rational genome-scale engineering and synthetic biology. PMID:19946878

  18. A new time-frequency method to reveal quantum dynamics of atomic hydrogen in intense laser pulses: Synchrosqueezing transform

    SciTech Connect

    Sheu, Yae-lin; Hsu, Liang-Yan; Wu, Hau-tieng; Li, Peng-Cheng; Chu, Shih-I

    2014-11-15

    This study introduces a new adaptive time-frequency (TF) analysis technique, the synchrosqueezing transform (SST), to explore the dynamics of a laser-driven hydrogen atom at an ab initio level, upon which we have demonstrated its versatility as a new viable venue for further exploring quantum dynamics. For a signal composed of oscillatory components which can be characterized by instantaneous frequency, the SST enables rendering the decomposed signal based on the phase information inherited in the linear TF representation with mathematical support. Compared with the classical type of TF methods, the SST clearly depicts several intrinsic quantum dynamical processes such as selection rules, AC Stark effects, and high harmonic generation.

  19. Ti α - ω phase transformation and metastable structure, revealed by the solid-state nudged elastic band method

    NASA Astrophysics Data System (ADS)

    Zarkevich, Nikolai; Johnson, Duane D.

    Titanium is on of the four most utilized structural metals, and, hence, its structural changes and potential metastable phases under stress are of considerable importance. Using DFT+U combined with the generalized solid-state nudged elastic band (SS-NEB) method, we consider the pressure-driven transformation between Ti α and ω phases, and find an intermediate metastable body-centered orthorhombic (bco) structure of lower density. We verify its stability, assess the phonons and electronic structure, and compare computational results to experiment. Interestingly, standard density functional theory (DFT) yields the ω phase as the Ti ground state, in contradiction to the observed α phase at low pressure and temperature. We correct this by proper consideration of the strongly correlated d-electrons, and utilize DFT+U method in the SS-NEB to obtain the relevant transformation pathway and structures. We use methods developed with support by the U.S. Department of Energy (DE-FG02-03ER46026 and DE-AC02-07CH11358). Ames Laboratory is operated for the DOE by Iowa State University under Contract DE-AC02-07CH11358.

  20. Transformation and Immobilization of Chromium by Arbuscular Mycorrhizal Fungi as Revealed by SEM-EDS, TEM-EDS, and XAFS.

    PubMed

    Wu, Songlin; Zhang, Xin; Sun, Yuqing; Wu, Zhaoxiang; Li, Tao; Hu, Yajun; Su, Dan; Lv, Jitao; Li, Gang; Zhang, Zhensong; Zheng, Lirong; Zhang, Jing; Chen, Baodong

    2015-12-15

    Arbuscular mycorrhizal fungi (AMF), ubiquitous soil fungi that form symbiotic relationships with the majority of terrestrial plants, are known to play an important role in plant tolerance to chromium (Cr) contamination. However, the underlying mechanisms, especially the direct influences of AMF on the translocation and transformation of Cr in the soil-plant continuum, are still unresolved. In a two-compartment root-organ cultivation system, the extraradical mycelium (ERM) of mycorrhizal roots was treated with 0.05 mmol L(-1) Cr(VI) for 12 days to investigate the uptake, translocation, and transformation of Cr(VI) by AMF using inductively coupled plasma mass spectrometry (ICP-MS), scanning electron microscopy equipped with energy-dispersive spectroscopy (SEM-EDS), transmission electron microscopy equipped with energy-dispersive spectroscopy (TEM-EDS), and X-ray-absorption fine structure (XAFS) technologies. The results indicated that AMF can immobilize quantities of Cr via reduction of Cr(VI) to Cr(III), forming Cr(III)-phosphate analogues, likely on the fungal surface. Besides this, we also confirmed that the extraradical mycelium (ERM) can actively take up Cr [either in the form of Cr(VI) or Cr(III)] and transport Cr [potentially in the form of Cr(III)-histidine analogues] to mycorrhizal roots but immobilize most of the Cr(III) in the fungal structures. Based on an X-ray absorption near-edge spectroscopy analysis of Cr(VI)-treated roots, we proposed that the intraradical fungal structures can also immobilize Cr within mycorrhizal roots. Our findings confirmed the immobilization of Cr by AMF, which plays an essential role in the Cr(VI) tolerance of AM symbioses. PMID:26551890

  1. Sources of distortion product otoacoustic emissions revealed by suppression experiments and inverse fast Fourier transforms in normal ears.

    PubMed

    Konrad-Martin, D; Neely, S T; Keefe, D H; Dorn, P A; Gorga, M P

    2001-06-01

    Primary and secondary sources combine to produce the 2f1-f2 distortion product otoacoustic emission (DPOAE) measured in the ear canals of humans. DPOAEs were obtained in nine normal-hearing subjects using a fixed-f2 paradigm in which f1 was varied. The f2 was 2 or 4 kHz, and absolute and relative primary levels were varied. Data were obtained with and without a third tone (f3) placed 15.6 Hz below 2f1-f2. The level of f3 was varied in order to suppress the stimulus frequency otoacoustic emission (SFOAE) coming from the 2f1-f2 place. These data were converted from the complex frequency domain into an equivalent time representation using an inverse fast Fourier transform (IFFT). IFFTs of unsuppressed DPOAE data were characterized by two or more peaks. Relative amplitudes of these peaks depended on overall primary level and on primary-level differences. The suppressor eliminated later peaks, but early peaks remained relatively unaltered. Results are interpreted to mean that the DPOAE measured in humans includes components from the f2 place (intermodulation distortion) and DP place (in the form of a SFOAE). These findings build on previous work by providing evidence that multiple peaks in the IFFT are due to a secondary source at the DP place. PMID:11425129

  2. Integrative Network Analysis Combined with Quantitative Phosphoproteomics Reveals Transforming Growth Factor-beta Receptor type-2 (TGFBR2) as a Novel Regulator of Glioblastoma Stem Cell Properties.

    PubMed

    Narushima, Yuta; Kozuka-Hata, Hiroko; Koyama-Nasu, Ryo; Tsumoto, Kouhei; Inoue, Jun-ichiro; Akiyama, Tetsu; Oyama, Masaaki

    2016-03-01

    Glioblastoma is one of the most malignant brain tumors with poor prognosis and their development and progression are known to be driven by glioblastoma stem cells. Although glioblastoma stem cells lose their cancer stem cell properties during cultivation in serum-containing medium, little is known about the molecular mechanisms regulating signaling alteration in relation to reduction of stem cell-like characteristics. To elucidate the global phosphorylation-related signaling events, we performed a SILAC-based quantitative phosphoproteome analysis of serum-induced dynamics in glioblastoma stem cells established from the tumor tissues of the patient. Among a total of 2876 phosphorylation sites on 1584 proteins identified in our analysis, 732 phosphorylation sites on 419 proteins were regulated through the alteration of stem cell-like characteristics. The integrative computational analyses based on the quantified phosphoproteome data revealed the relevant changes of phosphorylation levels regarding the proteins associated with cytoskeleton reorganization such as Rho family GTPase and Intermediate filament signaling, in addition to transforming growth factor-β receptor type-2 (TGFBR2) as a prominent upstream regulator involved in the serum-induced phosphoproteome regulation. The functional association of transforming growth factor-β receptor type-2 with stem cell-like properties was experimentally validated through signaling perturbation using the corresponding inhibitors, which indicated that transforming growth factor-β receptor type-2 could play an important role as a novel cell fate determinant in glioblastoma stem cell regulation. PMID:26670566

  3. Probing the Functional Diversity of Global Pristine Soil Communities with 3-Chlorobenzoate Reveals that Communities of Generalists Dominate Catabolic Transformation

    PubMed Central

    Rhodes, Albert N.; Fulthorpe, Roberta R.

    2013-01-01

    Understanding of functional diversity of microbial populations has lagged description of their molecular diversity. Differences in substrate specificity, kinetics, products, and regulation can dramatically influence phenotypic variation among closely related strains, features that are missed when the strains studied are the fastest-growing and most easily isolated from serial enrichments. To investigate the broader bacterial diversity underlying degradation of anthropogenic chemicals in nature, we studied the 3-chlorobenzoate (3-CBA) degradation rate in a collection of aerobic 3-CBA degraders previously isolated from undisturbed soils in two representative ecosystems: (i) Mediterranean sclerophyllous woodlands in California, Chile, South Africa, and Australia and (ii) boreal forests in Canada and Russia. The majority of isolates degraded 3-CBA slowly and did not completely mineralize 1.0 mM 3-CBA within 1 week. Those with intermediate degradation rates had incomplete degradation pathways and produced colored intermediates indicative of chlorocatechol, a product likely metabolized by other members of the community. About 10% of the isolates grew rapidly and mineralized greater than 90% of the 3-CBA, but because of population heterogeneity in soil, they are likely not large contributors to a soil's total transformation capacity. This suggests that xenobiotic degradation in nature is carried out by a community of cometabolic generalists and not by the efficient specialists that have been traditionally studied in the laboratory. A subset of 58 genotypically distinct strains able to degrade >80% of the 3-CBA was examined for their catabolic versatility using 45 different compounds: mono- and dichlorinated benzoates, phenols, anilines, toluenes, nitrobenzenes, chlorobenzenes, and 2,4-dichlorophenoxyacetic acid. The isolates degraded from 2 to more than 30 compounds with a median of 7, but there was no correlation to habitat of isolation or 3-CBA activity. However, these

  4. Methods in molecular cardiology: in silico cloning

    PubMed Central

    Passier, R.; Doevendans, P.A.

    2004-01-01

    Advancements in sequencing technology have made it possible to obtain more information about the DNA sequence, structure and the transcript products of the genome from different species. This information is collected in DNA databases. These databases contain many genes of which the functions have not yet been discovered. By using online biotechnology tools novel genes and their transcripts can be identified. The identification of novel genes using DNA database analysis is referred to as in silico cloning. In silico cloning may not only provide new information on genes and their biological function, it may also lead to identification of molecular targets for drug discovery activities. In this review we describe the process of in silico cloning and its application in biomedical research. ImagesFigure 1Figure 3 PMID:25696371

  5. In Silico Analysis of FMR1 Gene Missense SNPs.

    PubMed

    Tekcan, Akin

    2016-06-01

    The FMR1 gene, a member of the fragile X-related gene family, is responsible for fragile X syndrome (FXS). Missense single-nucleotide polymorphisms (SNPs) are responsible for many complex diseases. The effect of FMR1 gene missense SNPs is unknown. The aim of this study, using in silico techniques, was to analyze all known missense mutations that can affect the functionality of the FMR1 gene, leading to mental retardation (MR) and FXS. Data on the human FMR1 gene were collected from the Ensembl database (release 81), National Centre for Biological Information dbSNP Short Genetic Variations database, 1000 Genomes Browser, and NHLBI Exome Sequencing Project Exome Variant Server. In silico analysis was then performed. One hundred-twenty different missense SNPs of the FMR1 gene were determined. Of these, 11.66 % of the FMR1 gene missense SNPs were in highly conserved domains, and 83.33 % were in domains with high variety. The results of the in silico prediction analysis showed that 31.66 % of the FMR1 gene SNPs were disease related and that 50 % of SNPs had a pathogenic effect. The results of the structural and functional analysis revealed that although the R138Q mutation did not seem to have a damaging effect on the protein, the G266E and I304N SNPs appeared to disturb the interaction between the domains and affect the function of the protein. This is the first study to analyze all missense SNPs of the FMR1 gene. The results indicate the applicability of a bioinformatics approach to FXS and other FMR1-related diseases. I think that the analysis of FMR1 gene missense SNPs using bioinformatics methods would help diagnosis of FXS and other FMR1-related diseases. PMID:26880065

  6. Relationship between expression of serendipity alpha and cellularisation of the Drosophila embryo as revealed by interspecific transformation.

    PubMed

    Ibnsouda, S; Schweisguth, F; de Billy, G; Vincent, A

    1993-10-01

    A dramatic reorganization of the cytoskeleton underlies the cellularisation of the syncytial Drosophila embryo. Formation of a regular network of acto-myosin filaments, providing a structural framework, and possibly a contractile force as well, appears essential for the synchronous invagination of the plasma membrane between adjacent nuclei. The serendipity alpha (sry alpha) gene is required for this complete reorganization of the microfilaments at the onset of membrane invagination. We compare here the structure and expression of sry alpha between D. pseudoobscura, D. subobscura and D. melanogaster. Interspersion of evolutionarily highly conserved and divergent regions is observed in the protein. One such highly conserved region shows sequence similarities to a motif found in proteins of the ezrin-radixin-moesin (ERM) family. Four 7-13 bp motifs are conserved in the 5' promoter region; two of these are also found, and at the same position relative to the TATA box, in nullo, another zygotic gene recently shown to be involved in cellularisation. The compared patterns of expression of D. melanogaster sry alpha and nullo, and D. pseudoobscura sry alpha reveal a complex regulation of the spatiotemporal accumulation of their transcripts. The D. pseudoobscura sry alpha gene is able to rescue the cellularisation defects associated with a complete loss of sry alpha function in D. melanogaster embryos, even though species-specific aspects of its expression are maintained. Despite their functional homologies, the D. melanogaster and D. pseudoobscura sry alpha RNAs have different subcellular localisations, suggesting that this specific localization has no conserved role in targeting the sry alpha protein to the apical membranes. PMID:8287797

  7. High Accuracy in Silico Sulfotransferase Models*

    PubMed Central

    Cook, Ian; Wang, Ting; Falany, Charles N.; Leyh, Thomas S.

    2013-01-01

    Predicting enzymatic behavior in silico is an integral part of our efforts to understand biology. Hundreds of millions of compounds lie in targeted in silico libraries waiting for their metabolic potential to be discovered. In silico “enzymes” capable of accurately determining whether compounds can inhibit or react is often the missing piece in this endeavor. This problem has now been solved for the cytosolic sulfotransferases (SULTs). SULTs regulate the bioactivities of thousands of compounds—endogenous metabolites, drugs and other xenobiotics—by transferring the sulfuryl moiety (SO3) from 3′-phosphoadenosine 5′-phosphosulfate to the hydroxyls and primary amines of these acceptors. SULT1A1 and 2A1 catalyze the majority of sulfation that occurs during human Phase II metabolism. Here, recent insights into the structure and dynamics of SULT binding and reactivity are incorporated into in silico models of 1A1 and 2A1 that are used to identify substrates and inhibitors in a structurally diverse set of 1,455 high value compounds: the FDA-approved small molecule drugs. The SULT1A1 models predict 76 substrates. Of these, 53 were known substrates. Of the remaining 23, 21 were tested, and all were sulfated. The SULT2A1 models predict 22 substrates, 14 of which are known substrates. Of the remaining 8, 4 were tested, and all are substrates. The models proved to be 100% accurate in identifying substrates and made no false predictions at Kd thresholds of 100 μm. In total, 23 “new” drug substrates were identified, and new linkages to drug inhibitors are predicted. It now appears to be possible to accurately predict Phase II sulfonation in silico. PMID:24129576

  8. High-Throughput Genotyping of Green Algal Mutants Reveals Random Distribution of Mutagenic Insertion Sites and Endonucleolytic Cleavage of Transforming DNA[W][OPEN

    PubMed Central

    Zhang, Ru; Patena, Weronika; Armbruster, Ute; Gang, Spencer S.; Blum, Sean R.; Jonikas, Martin C.

    2014-01-01

    A high-throughput genetic screening platform in a single-celled photosynthetic eukaryote would be a transformative addition to the plant biology toolbox. Here, we present ChlaMmeSeq (Chlamydomonas MmeI-based insertion site Sequencing), a tool for simultaneous mapping of tens of thousands of mutagenic insertion sites in the eukaryotic unicellular green alga Chlamydomonas reinhardtii. We first validated ChlaMmeSeq by in-depth characterization of individual insertion sites. We then applied ChlaMmeSeq to a mutant pool and mapped 11,478 insertions, covering 39% of annotated protein coding genes. We observe that insertions are distributed in a manner largely indistinguishable from random, indicating that mutants in nearly all genes can be obtained efficiently. The data reveal that sequence-specific endonucleolytic activities cleave the transforming DNA and allow us to propose a simple model to explain the origin of the poorly understood exogenous sequences that sometimes surround insertion sites. ChlaMmeSeq is quantitatively reproducible, enabling its use for pooled enrichment screens and for the generation of indexed mutant libraries. Additionally, ChlaMmeSeq allows genotyping of hits from Chlamydomonas screens on an unprecedented scale, opening the door to comprehensive identification of genes with roles in photosynthesis, algal lipid metabolism, the algal carbon-concentrating mechanism, phototaxis, the biogenesis and function of cilia, and other processes for which C. reinhardtii is a leading model system. PMID:24706510

  9. Towards in silico prediction of immunogenic epitopes.

    PubMed

    Flower, Darren R

    2003-12-01

    As torrents of new data now emerge from microbial genomics, bioinformatic prediction of immunogenic epitopes remains challenging but vital. In silico methods often produce paradoxically inconsistent results: good prediction rates on certain test sets but not others. The inherent complexity of immune presentation and recognition processes complicates epitope prediction. Two encouraging developments - data driven artificial intelligence sequence-based methods for epitope prediction and molecular modeling methods based on three-dimensional protein structures - offer hope for the future. PMID:14644141

  10. Single-Molecule Experiments in Vitro and in Silico

    NASA Astrophysics Data System (ADS)

    Sotomayor, Marcos; Schulten, Klaus

    2007-05-01

    Single-molecule force experiments in vitro enable the characterization of the mechanical response of biological matter at the nanometer scale. However, they do not reveal the molecular mechanisms underlying mechanical function. These can only be readily studied through molecular dynamics simulations of atomic structural models: “in silico” (by computer analysis) single-molecule experiments. Steered molecular dynamics simulations, in which external forces are used to explore the response and function of macromolecules, have become a powerful tool complementing and guiding in vitro single-molecule experiments. The insights provided by in silico experiments are illustrated here through a review of recent research in three areas of protein mechanics: elasticity of the muscle protein titin and the extracellular matrix protein fibronectin; linker-mediated elasticity of the cytoskeleton protein spectrin; and elasticity of ankyrin repeats, a protein module found ubiquitously in cells but with an as-yet unclear function.

  11. In silico PCR primer designing and validation.

    PubMed

    Kumar, Anil; Chordia, Nikita

    2015-01-01

    Polymerase chain reaction (PCR) is an enzymatic reaction whose efficiency and sensitivity largely depend on the efficiency of the primers that are used for the amplification of a concerned gene/DNA fragment. Selective amplification of nucleic acid molecules initially present in minute quantities provides a powerful tool for analyzing nucleic acids. In silico method helps in designing primers. There are various programs available for PCR primer design. Here we described designing of primers using web-based tools like "Primer3" and "Web Primer". For designing the primer, DNA template sequence is required that can be taken from any of the available sequence databases, e.g., RefSeq database. The in silico validation can be carried out using BLAST tool and Gene Runner software, which check their efficiency and specificity. Thereafter, the primers designed in silico can be validated in the wet lab. After that, these validated primers can be synthesized for use in the amplification of concerned gene/DNA fragment. PMID:25697657

  12. In Silico Modeling of Geobacter Species.

    SciTech Connect

    Lovley, Derek, R.

    2008-01-29

    This project employed a combination of in silico modeling and physiological studies to begin the construction of models that could predict the activity of Geobacter species under different environmental conditions. A major accomplishment of the project was the development of the first genome-based models of organisms known environmental relevance. This included the modeling of two Geobacter species and two species of Pelobacter. Construction of these models required increased sophistication in the annotation of the original draft genomes as well as collection of physiological data on growth yields, cell composition, and metabolic reactions. Biochemical studies were conducted to determine whether proposed enzymatic reactions were in fact expressed. During this process we developed an Automodel Pipeline process to accelerate future model development of other environmentally relevant organisms by using bioinformatics techniques to leverage predicted protein sequences and the Genomatica database containing a collection of well-curated metabolic models. The Automodel Pipeline was also used for iterative updating of the primary Geobacter model of G. sulfurreducens to expand metabolic functions or to add alternative pathways. Although each iteration of the model does not lead to another publication, it is an invaluable resource for hypothesis development and evaluation of experimental data. In order to develop a more accurate G. sulfurreducens model, a series of physiological studies that could be analyzed in the context of the model were carried out. For example, previous field trials of in situ uranium bioremediation demonstrated that Geobacter species face an excess of electron donor and a limitation of electron acceptor near the point of acetate injection into the groundwater. Therefore, a model-based analysis of electron acceptor limitation physiology was conducted and model predictions were compared with growth observed in chemostats. Iterative studies resulted in

  13. In silico toxicology for the pharmaceutical sciences

    SciTech Connect

    Valerio, Luis G.

    2009-12-15

    The applied use of in silico technologies (a.k.a. computational toxicology, in silico toxicology, computer-assisted tox, e-tox, i-drug discovery, predictive ADME, etc.) for predicting preclinical toxicological endpoints, clinical adverse effects, and metabolism of pharmaceutical substances has become of high interest to the scientific community and the public. The increased accessibility of these technologies for scientists and recent regulations permitting their use for chemical risk assessment supports this notion. The scientific community is interested in the appropriate use of such technologies as a tool to enhance product development and safety of pharmaceuticals and other xenobiotics, while ensuring the reliability and accuracy of in silico approaches for the toxicological and pharmacological sciences. For pharmaceutical substances, this means active and impurity chemicals in the drug product may be screened using specialized software and databases designed to cover these substances through a chemical structure-based screening process and algorithm specific to a given software program. A major goal for use of these software programs is to enable industry scientists not only to enhance the discovery process but also to ensure the judicious use of in silico tools to support risk assessments of drug-induced toxicities and in safety evaluations. However, a great amount of applied research is still needed, and there are many limitations with these approaches which are described in this review. Currently, there is a wide range of endpoints available from predictive quantitative structure-activity relationship models driven by many different computational software programs and data sources, and this is only expected to grow. For example, there are models based on non-proprietary and/or proprietary information specific to assessing potential rodent carcinogenicity, in silico screens for ICH genetic toxicity assays, reproductive and developmental toxicity, theoretical

  14. Lower nanometer-scale size limit for the deformation of a metallic glass by shear transformations revealed by quantitative AFM indentation

    PubMed Central

    Bennewitz, Roland

    2015-01-01

    Summary We combine non-contact atomic force microscopy (AFM) imaging and AFM indentation in ultra-high vacuum to quantitatively and reproducibly determine the hardness and deformation mechanisms of Pt(111) and a Pt57.5Cu14.7Ni5.3P22.5 metallic glass with unprecedented spatial resolution. Our results on plastic deformation mechanisms of crystalline Pt(111) are consistent with the discrete mechanisms established for larger scales: Plasticity is mediated by dislocation gliding and no rate dependence is observed. For the metallic glass we have discovered that plastic deformation at the nanometer scale is not discrete but continuous and localized around the indenter, and does not exhibit rate dependence. This contrasts with the observation of serrated, rate-dependent flow of metallic glasses at larger scales. Our results reveal a lower size limit for metallic glasses below which shear transformation mechanisms are not activated by indentation. In the case of metallic glass, we conclude that the energy stored in the stressed volume during nanometer-scale indentation is insufficient to account for the interfacial energy of a shear band in the glassy matrix. PMID:26425424

  15. Functional phosphoproteomic analysis reveals cold-shock domain protein A to be a Bcr-Abl effector-regulating proliferation and transformation in chronic myeloid leukemia

    PubMed Central

    Sears, D; Luong, P; Yuan, M; Nteliopoulos, G; Man, Y K S; Melo, J V; Basu, S

    2010-01-01

    One proposed strategy to suppress the proliferation of imatinib-resistant cells in chronic myeloid leukemia (CML) is to inhibit key proteins downstream of Bcr-Abl. The PI3K/Akt pathway is activated by Bcr-Abl and is specifically required for the growth of CML cells. To identify targets of this pathway, we undertook a proteomic screen and identified several proteins that differentially bind 14-3-3, dependent on Bcr-Abl kinase activity. An siRNA screen of candidates selected by bioinformatics analysis reveals cold-shock domain protein A (CSDA), shown previously to regulate cell cycle progression in epithelial cells, to be a positive regulator of proliferation in a CML cell line. We show that Akt can phosphorylate the serine 134 residue of CSDA but, downstream of Bcr-Abl activity, this modification is mediated through the activation of MEK/p90 ribosomal S6 kinase (RSK) signaling. Inhibition of RSK, similarly to treatment with imatinib, blocked proliferation specifically in Bcr-Abl-positive leukemia cell lines, as well as cells from CML patients. Furthermore, these primary CML cells showed an increase in CSDA phosphorylation. Expression of a CSDA phospho-deficient mutant resulted in the decrease of Bcr-Abl-dependent transformation in Rat1 cells. Our results support a model whereby phosphorylation of CSDA downstream of Bcr-Abl enhances proliferation in CML cells to drive leukemogenesis. PMID:21368869

  16. Hydrothermal synthesis of silico-manganese nanohybrid for Cu(II) adsorption from aqueous solution

    NASA Astrophysics Data System (ADS)

    Zhu, Qiufeng; Wang, Liting; An, Zehuan; Ye, Hong; Feng, Xudong

    2016-05-01

    A novel silico-manganese nanohybrid adsorbent (SMNA) was synthesized by a facile hydrothermal method, and characterized by X-ray diffraction (XRD), transmission electron microscopy (TEM), nitrogen adsorption-desorption, Fourier transform infrared spectroscopy (FT-IR) and zeta potential measurement. The adsorption of Cu(II) ions from aqueous solution on the SMNA was investigated with variations in contact time, pH and initial Cu(II) concentration. The results showed that hydrothermal method would generate nanowire/nanorod incomplete crystallite (δ-MnO2) adsorbent. The adsorption of Cu(II) onto SMNA increased sharply within 25 min and reached equilibrium gradually. The maximum adsorption capacities of SMNA for Cu(II) were ∼40-88 mg g-1, which was lower than δ-MnO2 (92.42 mg g-1) but had a lower pH dependency. As compared with δ-MnO2, higher adsorption capacities of SMNA (7.5-15 wt% of silica doping amount) for Cu(II) could be observed when pH of the aqueous solution was low (<4). The pseudo-second-order model was the best choice to describe the adsorption behavior of Cu(II) onto SMNA, suggesting that the removal of Cu(II) by the as-prepared adsorbents was dominated by migration of Cu(II). The possibility of Cu(II) recovery was also investigated and it revealed that SMNA was a promising recyclable adsorbent for removal of heavy metal ions in water and wastewater treatment.

  17. Ternary Complex of Transforming Growth Factor-[beta]1 Reveals Isoform-specific Ligand Recognition and Receptor Recruitment in the Superfamily

    SciTech Connect

    Radaev, Sergei; Zou, Zhongcheng; Huang, Tao; Lafer, Eileen M.; Hinck, Andrew P.; Sun, Peter D.

    2010-11-03

    Transforming growth factor (TGF)-{beta}1, -{beta}2, and -{beta}3 are 25-kDa homodimeric polypeptides that play crucial nonoverlapping roles in embryogenesis, tissue development, carcinogenesis, and immune regulation. Here we report the 3.0-{angstrom} resolution crystal structure of the ternary complex between human TGF-{beta}1 and the extracellular domains of its type I and type II receptors, T{beta}RI and T{beta}RII. The TGF-{beta}1 ternary complex structure is similar to previously reported TGF-{beta}3 complex except with a 10{sup o} rotation in T{beta}RI docking orientation. Quantitative binding studies showed distinct kinetics between the receptors and the isoforms of TGF-{beta}. T{beta}RI showed significant binding to TGF-{beta}2 and TGF-{beta}3 but not TGF-{beta}1, and the binding to all three isoforms of TGF-{beta} was enhanced considerably in the presence of T{beta}RII. The preference of TGF-{beta}2 to T{beta}RI suggests a variation in its receptor recruitment in vivo. Although TGF-{beta}1 and TGF-{beta}3 bind and assemble their ternary complexes in a similar manner, their structural differences together with differences in the affinities and kinetics of their receptor binding may underlie their unique biological activities. Structural comparisons revealed that the receptor-ligand pairing in the TGF-{beta} superfamily is dictated by unique insertions, deletions, and disulfide bonds rather than amino acid conservation at the interface. The binding mode of T{beta}RII on TGF-{beta} is unique to TGF-{beta}s, whereas that of type II receptor for bone morphogenetic protein on bone morphogenetic protein appears common to all other cytokines in the superfamily. Further, extensive hydrogen bonds and salt bridges are present at the high affinity cytokine-receptor interfaces, whereas hydrophobic interactions dominate the low affinity receptor-ligand interfaces.

  18. In Silico Models for Ecotoxicity of Pharmaceuticals.

    PubMed

    Roy, Kunal; Kar, Supratik

    2016-01-01

    Pharmaceuticals and their active metabolites are one of the significantly emerging environmental toxicants. The major routes of entry of pharmaceuticals into the environment are industries, hospitals, or direct disposal of unwanted or expired drugs made by the patient. The most important and distinct features of pharmaceuticals are that they are deliberately designed to have an explicit mode of action and designed to exert an effect on humans and other living systems. This distinctive feature makes pharmaceuticals and their metabolites different from other chemicals, and this necessitates the evaluation of the direct effects of pharmaceuticals in various environmental compartments as well as to living systems. In this background, the alarming situation of ecotoxicity of diverse pharmaceuticals have forced government and nongovernment regulatory authorities to recommend the application of in silico methods to provide quick information about the risk assessment and fate properties of pharmaceuticals as well as their ecological and indirect human health effects. This chapter aims to offer information regarding occurrence of pharmaceuticals in the environment, their persistence, environmental fate, and toxicity as well as application of in silico methods to provide information about the basic risk management and fate prediction of pharmaceuticals in the environment. Brief ideas about toxicity endpoints, available ecotoxicity databases, and expert systems employed for rapid toxicity predictions of ecotoxicity of pharmaceuticals are also discussed. PMID:27311470

  19. In silico methods for drug repurposing and pharmacology.

    PubMed

    Hodos, Rachel A; Kidd, Brian A; Shameer, Khader; Readhead, Ben P; Dudley, Joel T

    2016-05-01

    Data in the biological, chemical, and clinical domains are accumulating at ever-increasing rates and have the potential to accelerate and inform drug development in new ways. Challenges and opportunities now lie in developing analytic tools to transform these often complex and heterogeneous data into testable hypotheses and actionable insights. This is the aim of computational pharmacology, which uses in silico techniques to better understand and predict how drugs affect biological systems, which can in turn improve clinical use, avoid unwanted side effects, and guide selection and development of better treatments. One exciting application of computational pharmacology is drug repurposing-finding new uses for existing drugs. Already yielding many promising candidates, this strategy has the potential to improve the efficiency of the drug development process and reach patient populations with previously unmet needs such as those with rare diseases. While current techniques in computational pharmacology and drug repurposing often focus on just a single data modality such as gene expression or drug-target interactions, we argue that methods such as matrix factorization that can integrate data within and across diverse data types have the potential to improve predictive performance and provide a fuller picture of a drug's pharmacological action. WIREs Syst Biol Med 2016, 8:186-210. doi: 10.1002/wsbm.1337 For further resources related to this article, please visit the WIREs website. PMID:27080087

  20. In Vivo and In Silico Investigation Into Mechanisms of Frequency Dependence of Repolarization Alternans in Human Ventricular Cardiomyocytes

    PubMed Central

    Zhou, Xin; Bueno-Orovio, Alfonso; Orini, Michele; Hanson, Ben; Hayward, Martin; Taggart, Peter; Lambiase, Pier D.; Burrage, Kevin

    2016-01-01

    Rationale: Repolarization alternans (RA) are associated with arrhythmogenesis. Animal studies have revealed potential mechanisms, but human-focused studies are needed. RA generation and frequency dependence may be determined by cell-to-cell variability in protein expression, which is regulated by genetic and external factors. Objective: To characterize in vivo RA in human and to investigate in silico using human models, the ionic mechanisms underlying the frequency-dependent differences in RA behavior identified in vivo. Methods and Results: In vivo electrograms were acquired at 240 sites covering the epicardium of 41 patients at 6 cycle lengths (600–350 ms). In silico investigations were conducted using a population of biophysically detailed human models incorporating variability in protein expression and calibrated using in vivo recordings. Both in silico and in vivo, 2 types of RA were identified, with Fork- and Eye-type restitution curves, based on RA persistence or disappearance, respectively, at fast pacing rates. In silico simulations show that RA are strongly correlated with fluctuations in sarcoplasmic reticulum calcium, because of strong release and weak reuptake. Large L-type calcium current conductance is responsible for RA disappearance at fast frequencies in Eye-type (30% larger in Eye-type versus Fork-type; P<0.01), because of sarcoplasmic reticulum Ca2+ ATPase pump potentiation caused by frequency-induced increase in intracellular calcium. Large Na+/Ca2+ exchanger current is the main driver in translating Ca2+ fluctuations into RA. Conclusions: In human in vivo and in silico, 2 types of RA are identified, with RA persistence/disappearance as frequency increases. In silico, L-type calcium current and Na+/Ca2+ exchanger current determine RA human cell-to-cell differences through intracellular and sarcoplasmic reticulum calcium regulation. PMID:26602864

  1. In Silico-Based High-Throughput Screen for Discovery of Novel Combinations for Tuberculosis Treatment

    PubMed Central

    Singh, Ragini; Ramachandran, Vasanthi; Shandil, Radha; Sharma, Sreevalli; Khandelwal, Swati; Karmarkar, Malancha; Kumar, Naveen; Solapure, Suresh; Saralaya, Ramanatha; Nanduri, Robert; Panduga, Vijender; Reddy, Jitendar; Prabhakar, K. R.; Rajagopalan, Swaminathan; Rao, Narasimha; Narayanan, Shridhar; Anandkumar, Anand; Datta, Santanu

    2015-01-01

    There are currently 18 drug classes for the treatment of tuberculosis, including those in the development pipeline. An in silico simulation enabled combing the innumerably large search space to derive multidrug combinations. Through the use of ordinary differential equations (ODE), we constructed an in silico kinetic platform in which the major metabolic pathways in Mycobacterium tuberculosis and the mechanisms of the antituberculosis drugs were integrated into a virtual proteome. The optimized model was used to evaluate 816 triplets from the set of 18 drugs. The experimentally derived cumulative fractional inhibitory concentration (∑FIC) value was within twofold of the model prediction. Bacterial enumeration revealed that a significant number of combinations that were synergistic for growth inhibition were also synergistic for bactericidal effect. The in silico-based screen provided new starting points for testing in a mouse model of tuberculosis, in which two novel triplets and five novel quartets were significantly superior to the reference drug triplet of isoniazid, rifampin, and ethambutol (HRE) or the quartet of HRE plus pyrazinamide (HREZ). PMID:26149995

  2. In Silico Strategies for Modeling Stereoselective Metabolism of Pyrethroids

    EPA Science Inventory

    In silico methods are invaluable tools to researchers seeking to understand and predict metabolic processes within PBPK models. Even though these methods have been successfully utilized to predict and quantify metabolic processes, there are many challenges involved. Stereochemica...

  3. In silico Therapeutics for Neurogenic Hypertension and Vasovagal Syncope

    PubMed Central

    Bojić, Tijana; Perović, Vladimir R.; Glišić, Sanja

    2016-01-01

    Neurocardiovascular diseases (NCVD) are the leading cause of death in the developed world and will remain so till 2020. In these diseases the pathologically changed nervous control of cardiovascular system has the central role. The actual NCV syndromes are neurogenic hypertension, representing the sympathetically mediated disorder, and vasovagal syncope, which is the vagally mediated disorders. Vasovagal syncope, the disease far from its etiological treatment, could benefit from recruiting and application of antimuscarinic drugs used in other parasympathetic disorders. The informational spectrum method (ISM), a method widely applied for the characterization of protein-protein interactions in the field of immunology, endocrinology and anti HIV drug discovery, was applied for the first time in the analysis of neurogenic hypertension and vasovagal syncope therapeutic targets. In silico analysis revealed the potential involvement of apelin in neurogenic hypertension. Applying the EIIP/ISM bioinformatics concept in investigation of drugs for treatment of vasovagal syncope suggests that 78% of tested antimuscarinic drugs could have anti vasovagal syncope effect. The presented results confirm that ISM is a promissing method for investigation of molecular mechanisms underlying pathophysiological proceses of NCV syndromes and discovery of therapeutics targets for their treatment. PMID:26834545

  4. In silico Therapeutics for Neurogenic Hypertension and Vasovagal Syncope.

    PubMed

    Bojić, Tijana; Perović, Vladimir R; Glišić, Sanja

    2015-01-01

    Neurocardiovascular diseases (NCVD) are the leading cause of death in the developed world and will remain so till 2020. In these diseases the pathologically changed nervous control of cardiovascular system has the central role. The actual NCV syndromes are neurogenic hypertension, representing the sympathetically mediated disorder, and vasovagal syncope, which is the vagally mediated disorders. Vasovagal syncope, the disease far from its etiological treatment, could benefit from recruiting and application of antimuscarinic drugs used in other parasympathetic disorders. The informational spectrum method (ISM), a method widely applied for the characterization of protein-protein interactions in the field of immunology, endocrinology and anti HIV drug discovery, was applied for the first time in the analysis of neurogenic hypertension and vasovagal syncope therapeutic targets. In silico analysis revealed the potential involvement of apelin in neurogenic hypertension. Applying the EIIP/ISM bioinformatics concept in investigation of drugs for treatment of vasovagal syncope suggests that 78% of tested antimuscarinic drugs could have anti vasovagal syncope effect. The presented results confirm that ISM is a promissing method for investigation of molecular mechanisms underlying pathophysiological proceses of NCV syndromes and discovery of therapeutics targets for their treatment. PMID:26834545

  5. Expression and In Silico Analysis of the Recombinant Bovine Papillomavirus E6 Protein as a Model for Viral Oncoproteins Studies

    PubMed Central

    Mazzuchelli-de-Souza, J.; Carvalho, R. F.; Ruiz, R. M.; Melo, T. C.; Araldi, R. P.; Carvalho, E.; Thompson, C. E.; Sircili, M. P.; Beçak, W.; Stocco, R. C.

    2013-01-01

    Bovine papillomaviruses (BPVs) are recognized as the causal agents of economical relevant diseases in cattle, associated with the development of tumors in skin and mucosa. The oncogenesis process is mainly associated with different viral oncoprotein expressions, which are involved in cell transformation. The expression and characterization of recombinant viral oncoproteins represent an attractive strategy to obtain biotechnological products as antibodies and potential vaccines, Thus, the aim of this work was to clone and express the BPV-1 and BPV-2 E6 recombinant proteins and perform in silico analysis in order to develop a strategy for the systematic study of other papillomaviruses oncoproteins. The results demonstrated that BPV-1 and BPV-2 E6 recombinant proteins were expressed and purified from bacterial system as well as its in silico analysis was performed in order to explore and predict biological characteristics of these proteins. PMID:23878806

  6. In silico selection of RNA aptamers

    PubMed Central

    Chushak, Yaroslav; Stone, Morley O.

    2009-01-01

    In vitro selection of RNA aptamers that bind to a specific ligand usually begins with a random pool of RNA sequences. We propose a computational approach for designing a starting pool of RNA sequences for the selection of RNA aptamers for specific analyte binding. Our approach consists of three steps: (i) selection of RNA sequences based on their secondary structure, (ii) generating a library of three-dimensional (3D) structures of RNA molecules and (iii) high-throughput virtual screening of this library to select aptamers with binding affinity to a desired small molecule. We developed a set of criteria that allows one to select a sequence with potential binding affinity from a pool of random sequences and developed a protocol for RNA 3D structure prediction. As verification, we tested the performance of in silico selection on a set of six known aptamer–ligand complexes. The structures of the native sequences for the ligands in the testing set were among the top 5% of the selected structures. The proposed approach reduces the RNA sequences search space by four to five orders of magnitude—significantly accelerating the experimental screening and selection of high-affinity aptamers. PMID:19465396

  7. In Silico Approaches for Predicting Adme Properties

    NASA Astrophysics Data System (ADS)

    Madden, Judith C.

    A drug requires a suitable pharmacokinetic profile to be efficacious in vivo in humans. The relevant pharmacokinetic properties include the absorption, distribution, metabolism, and excretion (ADME) profile of the drug. This chapter provides an overview of the definition and meaning of key ADME properties, recent models developed to predict these properties, and a guide as to how to select the most appropriate model(s) for a given query. Many tools using the state-of-the-art in silico methodology are now available to users, and it is anticipated that the continual evolution of these tools will provide greater ability to predict ADME properties in the future. However, caution must be exercised in applying these tools as data are generally available only for "successful" drugs, i.e., those that reach the marketplace, and little supplementary information, such as that for drugs that have a poor pharmacokinetic profile, is available. The possibilities of using these methods and possible integration into toxicity prediction are explored.

  8. In silico selection of RNA aptamers.

    PubMed

    Chushak, Yaroslav; Stone, Morley O

    2009-07-01

    In vitro selection of RNA aptamers that bind to a specific ligand usually begins with a random pool of RNA sequences. We propose a computational approach for designing a starting pool of RNA sequences for the selection of RNA aptamers for specific analyte binding. Our approach consists of three steps: (i) selection of RNA sequences based on their secondary structure, (ii) generating a library of three-dimensional (3D) structures of RNA molecules and (iii) high-throughput virtual screening of this library to select aptamers with binding affinity to a desired small molecule. We developed a set of criteria that allows one to select a sequence with potential binding affinity from a pool of random sequences and developed a protocol for RNA 3D structure prediction. As verification, we tested the performance of in silico selection on a set of six known aptamer-ligand complexes. The structures of the native sequences for the ligands in the testing set were among the top 5% of the selected structures. The proposed approach reduces the RNA sequences search space by four to five orders of magnitude--significantly accelerating the experimental screening and selection of high-affinity aptamers. PMID:19465396

  9. Predicting human blood viscosity in silico

    SciTech Connect

    Fedosov, Dmitry A.; Pan, Wenxiao; Caswell, Bruce; Gompper, Gerhard; Karniadakis, George E.

    2011-07-05

    Cellular suspensions such as blood are a part of living organisms and their rheological and flow characteristics determine and affect majority of vital functions. The rheological and flow properties of cell suspensions are determined by collective dynamics of cells, their structure or arrangement, cell properties and interactions. We study these relations for blood in silico using a mesoscopic particle-based method and two different models (multi-scale/low-dimensional) of red blood cells. The models yield accurate quantitative predictions of the dependence of blood viscosity on shear rate and hematocrit. We explicitly model cell aggregation interactions and demonstrate the formation of reversible rouleaux structures resulting in a tremendous increase of blood viscosity at low shear rates and yield stress, in agreement with experiments. The non-Newtonian behavior of such cell suspensions (e.g., shear thinning, yield stress) is analyzed and related to the suspension’s microstructure, deformation and dynamics of single cells. We provide the flrst quantitative estimates of normal stress differences and magnitude of aggregation forces in blood. Finally, the flexibility of the cell models allows them to be employed for quantitative analysis of a much wider class of complex fluids including cell, capsule, and vesicle suspensions.

  10. Transformation of a series of saturated isomeric steroidal diols by Aspergillus tamarii KITA reveals a precise stereochemical requirement for entrance into the lactonization pathway.

    PubMed

    Hunter, A Christy; Collins, Catherine; Dodd, Howard T; Dedi, Cinzia; Koussoroplis, Salomé-Juliette

    2010-11-01

    Four isomers of 5α-androstan-3,17-diol have been transformed by the filamentous fungus Aspergillus tamarii, an organism which has the ability to convert progesterone to testololactone in high yield through an endogenous four step enzymatic pathway. The only diol handled within the lactonization pathway was 5α-androstan-3α,17β-diol which, uniquely underwent oxidation of the 17β-alcohol to the 17-ketone prior to its Baeyer-Villiger oxidation and the subsequent production of 3α-hydroxy-17a-oxa-D-homo-5α-androstan-17-one. This demonstrated highly specific stereochemical requirements of the 17β-hydroxysteroid dehydrogenase for oxidation of this specific steroidal diol to occur. In contrast, the other three diols were transformed within the hydroxylation pathway resulting in functionalization at C-11β. Only 5α-androstan-3β,17α-diol could bind to the hydroxylase in multiple binding modes undergoing monohydroxylation in 6β and 7β positions. Evidence from this study has indicated that hydroxylation of saturated steroidal lactones may occur following binding of ring-D in its open form in which an α-alcohol is generated with close spatial parity to the C-17α hydroxyl position. All metabolites were isolated by column chromatography and were identified by (1)H, (13)C NMR and DEPT analysis and further characterized using infra-red, elemental analysis and accurate mass measurement. PMID:20832471

  11. Revealing martensitic transformation and α/β interface evolution in electron beam melting three-dimensional-printed Ti-6Al-4V

    PubMed Central

    Tan, Xipeng; Kok, Yihong; Toh, Wei Quan; Tan, Yu Jun; Descoins, Marion; Mangelinck, Dominique; Tor, Shu Beng; Leong, Kah Fai; Chua, Chee Kai

    2016-01-01

    As an important metal three-dimensional printing technology, electron beam melting (EBM) is gaining increasing attention due to its huge potential applications in aerospace and biomedical fields. EBM processing of Ti-6Al-4V as well as its microstructure and mechanical properties were extensively investigated. However, it is still lack of quantitative studies regarding its microstructural evolution, indicative of EBM thermal process. Here, we report α′ martensitic transformation and α/β interface evolution in varied printing thicknesses of EBM-printed Ti-6Al-4V block samples by means of atom probe tomography. Quantitative chemical composition analysis suggests a general phase transformation sequence. By increasing in-fill hatched thickness, elemental partitioning ratios arise and β volume fraction is increased. Furthermore, we observe kinetic vanadium segregation and aluminum depletion at interface front and the resultant α/β interface widening phenomenon. It may give rise to an increased α/β lattice mismatch and weakened α/β interfaces, which could account for the degraded strength as printing thickness increases. PMID:27185285

  12. Revealing martensitic transformation and α/β interface evolution in electron beam melting three-dimensional-printed Ti-6Al-4V

    NASA Astrophysics Data System (ADS)

    Tan, Xipeng; Kok, Yihong; Toh, Wei Quan; Tan, Yu Jun; Descoins, Marion; Mangelinck, Dominique; Tor, Shu Beng; Leong, Kah Fai; Chua, Chee Kai

    2016-05-01

    As an important metal three-dimensional printing technology, electron beam melting (EBM) is gaining increasing attention due to its huge potential applications in aerospace and biomedical fields. EBM processing of Ti-6Al-4V as well as its microstructure and mechanical properties were extensively investigated. However, it is still lack of quantitative studies regarding its microstructural evolution, indicative of EBM thermal process. Here, we report α‧ martensitic transformation and α/β interface evolution in varied printing thicknesses of EBM-printed Ti-6Al-4V block samples by means of atom probe tomography. Quantitative chemical composition analysis suggests a general phase transformation sequence. By increasing in-fill hatched thickness, elemental partitioning ratios arise and β volume fraction is increased. Furthermore, we observe kinetic vanadium segregation and aluminum depletion at interface front and the resultant α/β interface widening phenomenon. It may give rise to an increased α/β lattice mismatch and weakened α/β interfaces, which could account for the degraded strength as printing thickness increases.

  13. Revealing martensitic transformation and α/β interface evolution in electron beam melting three-dimensional-printed Ti-6Al-4V.

    PubMed

    Tan, Xipeng; Kok, Yihong; Toh, Wei Quan; Tan, Yu Jun; Descoins, Marion; Mangelinck, Dominique; Tor, Shu Beng; Leong, Kah Fai; Chua, Chee Kai

    2016-01-01

    As an important metal three-dimensional printing technology, electron beam melting (EBM) is gaining increasing attention due to its huge potential applications in aerospace and biomedical fields. EBM processing of Ti-6Al-4V as well as its microstructure and mechanical properties were extensively investigated. However, it is still lack of quantitative studies regarding its microstructural evolution, indicative of EBM thermal process. Here, we report α' martensitic transformation and α/β interface evolution in varied printing thicknesses of EBM-printed Ti-6Al-4V block samples by means of atom probe tomography. Quantitative chemical composition analysis suggests a general phase transformation sequence. By increasing in-fill hatched thickness, elemental partitioning ratios arise and β volume fraction is increased. Furthermore, we observe kinetic vanadium segregation and aluminum depletion at interface front and the resultant α/β interface widening phenomenon. It may give rise to an increased α/β lattice mismatch and weakened α/β interfaces, which could account for the degraded strength as printing thickness increases. PMID:27185285

  14. Crystal structure and in silico studies of dihydrodipicolinate synthase (DHDPS) from Aquifex aeolicus.

    PubMed

    Sridharan, Upasana; Ebihara, Akio; Kuramitsu, Seiki; Yokoyama, Shigeyuki; Kumarevel, Thirumananseri; Ponnuraj, Karthe

    2014-11-01

    Dihydrodipicolinate synthase (DHDPS, E.C.4.2.1.52) catalyzes the first committed step in the lysine biosynthetic pathway: the condensation of (S)-aspartate semialdehyde and pyruvate to form (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid. Since (S)-lysine biosynthesis does not occur in animals, DHDPS is an attractive target for rational antibiotic and herbicide design. Here, we report the crystal structure of DHDPS from a hyperthermophilic bacterium Aquifex aeolicus (AqDHDPS). L-Lysine is used as an important animal feed additive where the production is at the level of 1.5 million tons per year. The biotechnological manufacture of lysine has been going for more than 50 years which includes over synthesis and reverse engineering of DHDPS. AqDHDPS revealed a unique disulfide linkage which is not conserved in the homologues of AqDHDPS. In silico mutation of C139A and intermolecular ion-pair residues and the subsequent molecular dynamics simulation of the mutants showed that these residues are critical for the stability of AqDHDPS tetramer. MD simulations of AqDHDPS at three different temperatures (303, 363 and 393 K) revealed that the molecule is stable at 363 K. Thus, this structural and in silico study of AqDHDPS likely provides additional details towards the rational and structure-based design of hyper-L-lysine producing bacterial strains. PMID:24996798

  15. Revealing lithium-silicide phase transformations in nano-structured silicon-based lithium ion batteries via in situ NMR spectroscopy.

    PubMed

    Ogata, K; Salager, E; Kerr, C J; Fraser, A E; Ducati, C; Morris, A J; Hofmann, S; Grey, C P

    2014-01-01

    Nano-structured silicon anodes are attractive alternatives to graphitic carbons in rechargeable Li-ion batteries, owing to their extremely high capacities. Despite their advantages, numerous issues remain to be addressed, the most basic being to understand the complex kinetics and thermodynamics that control the reactions and structural rearrangements. Elucidating this necessitates real-time in situ metrologies, which are highly challenging, if the whole electrode structure is studied at an atomistic level for multiple cycles under realistic cycling conditions. Here we report that Si nanowires grown on a conducting carbon-fibre support provide a robust model battery system that can be studied by (7)Li in situ NMR spectroscopy. The method allows the (de)alloying reactions of the amorphous silicides to be followed in the 2nd cycle and beyond. In combination with density-functional theory calculations, the results provide insight into the amorphous and amorphous-to-crystalline lithium-silicide transformations, particularly those at low voltages, which are highly relevant to practical cycling strategies. PMID:24488002

  16. A novel mouse model for inhibition of DOHH-mediated hypusine modification reveals a crucial function in embryonic development, proliferation and oncogenic transformation

    PubMed Central

    Sievert, Henning; Pällmann, Nora; Miller, Katharine K.; Hermans-Borgmeyer, Irm; Venz, Simone; Sendoel, Ataman; Preukschas, Michael; Schweizer, Michaela; Boettcher, Steffen; Janiesch, P. Christoph; Streichert, Thomas; Walther, Reinhard; Hengartner, Michael O.; Manz, Markus G.; Brümmendorf, Tim H.; Bokemeyer, Carsten; Braig, Melanie; Hauber, Joachim; Duncan, Kent E.; Balabanov, Stefan

    2014-01-01

    The central importance of translational control by post-translational modification has spurred major interest in regulatory pathways that control translation. One such pathway uniquely adds hypusine to eukaryotic initiation factor 5A (eIF5A), and thereby affects protein synthesis and, subsequently, cellular proliferation through an unknown mechanism. Using a novel conditional knockout mouse model and a Caenorhabditis elegans knockout model, we found an evolutionarily conserved role for the DOHH-mediated second step of hypusine synthesis in early embryonic development. At the cellular level, we observed reduced proliferation and induction of senescence in 3T3 Dohh−/− cells as well as reduced capability for malignant transformation. Furthermore, mass spectrometry showed that deletion of DOHH results in an unexpected complete loss of hypusine modification. Our results provide new biological insight into the physiological roles of the second step of the hypusination of eIF5A. Moreover, the conditional mouse model presented here provides a powerful tool for manipulating hypusine modification in a temporal and spatial manner, to analyse both how this unique modification normally functions in vivo as well as how it contributes to different pathological conditions. PMID:24832488

  17. An In silico approach for the evaluation of DNA barcodes

    PubMed Central

    2010-01-01

    Background DNA barcoding is a key tool for assessing biodiversity in both taxonomic and environmental studies. Essential features of barcodes include their applicability to a wide spectrum of taxa and their ability to identify even closely related species. Several DNA regions have been proposed as barcodes and the region selected strongly influences the output of a study. However, formal comparisons between barcodes remained limited until now. Here we present a standard method for evaluating barcode quality, based on the use of a new bioinformatic tool that performs in silico PCR over large databases. We illustrate this approach by comparing the taxonomic coverage and the resolution of several DNA regions already proposed for the barcoding of vertebrates. To assess the relationship between in silico and in vitro PCR, we also developed specific primers amplifying different species of Felidae, and we tested them using both kinds of PCR Results Tests on specific primers confirmed the correspondence between in silico and in vitro PCR. Nevertheless, results of in silico and in vitro PCRs can be somehow different, also because tuning PCR conditions can increase the performance of primers with limited taxonomic coverage. The in silico evaluation of DNA barcodes showed a strong variation of taxonomic coverage (i.e., universality): barcodes based on highly degenerated primers and those corresponding to the conserved region of the Cyt-b showed the highest coverage. As expected, longer barcodes had a better resolution than shorter ones, which are however more convenient for ecological studies analysing environmental samples. Conclusions In silico PCR could be used to improve the performance of a study, by allowing the preliminary comparison of several DNA regions in order to identify the most appropriate barcode depending on the study aims. PMID:20637073

  18. In Silico Toxicology – Non-Testing Methods

    PubMed Central

    Raunio, Hannu

    2011-01-01

    In silico toxicology in its broadest sense means “anything that we can do with a computer in toxicology.” Many different types of in silico methods have been developed to characterize and predict toxic outcomes in humans and environment. The term non-testing methods denote grouping approaches, structure–activity relationship, and expert systems. These methods are already used for regulatory purposes and it is anticipated that their role will be much more prominent in the near future. This Perspective will delineate the basic principles of non-testing methods and evaluate their role in current and future risk assessment of chemical compounds. PMID:21772821

  19. Ultra-small lipid-dendrimer hybrid nanoparticles as a promising strategy for antibiotic delivery: In vitro and in silico studies.

    PubMed

    Sonawane, Sandeep J; Kalhapure, Rahul S; Rambharose, Sanjeev; Mocktar, Chunderika; Vepuri, Suresh B; Soliman, Mahmoud; Govender, Thirumala

    2016-05-17

    The purpose of this study was to explore the preparation of a new lipid-dendrimer hybrid nanoparticle (LDHN) system to effectively deliver vancomycin against methicillin-resistant Staphylococcus aureus (MRSA) infections. Spherical LDHNs with particle size, polydispersity index and zeta potential of 52.21±0.22nm, 0.105±0.01, and -14.2±1.49mV respectively were prepared by hot stirring and ultrasonication using Compritol 888 ATO, G4 PAMAM- succinamic acid dendrimer, and Kolliphor RH-40. Vancomycin encapsulation efficiency (%) in LDHNs was almost 4.5-fold greater than in lipid-polymer hybrid nanoparticles formulated using Eudragit RS 100. Differential scanning calorimetry and Fourier transform-infrared studies confirmed the formation of LDHNs. The interactions between the drug-dendrimer complex and lipid molecules using in silico modeling revealed the molecular mechanism behind the enhanced encapsulation and stability. Vancomycin was released from LDHNs over the period of 72h with zero order kinetics and super case II transport mechanism. The minimum inhibitory concentration (MIC) against S. aureus and MRSA were 15.62μg/ml and 7.81μg/ml respectively. Formulation showed sustained activity with MIC of 62.5μg/ml against S. aureus and 500μg/ml against MRSA at the end of 72 and 54h period respectively. The results suggest that the LDHN system can be an effective strategy to combat resistant infections. PMID:26992817

  20. Spatiotemporal relationships between growth and microtubule orientation as revealed in living root cells of Arabidopsis thaliana transformed with green-fluorescent-protein gene construct GFP-MBD

    NASA Technical Reports Server (NTRS)

    Granger, C. L.; Cyr, R. J.

    2001-01-01

    Arabidopsis thaliana plants were transformed with GFP-MBD (J. Marc et al., Plant Cell 10: 1927-1939, 1998) under the control of a constitutive (35S) or copper-inducible promoter. GFP-specific fluorescence distributions, levels, and persistence were determined and found to vary with age, tissue type, transgenic line, and individual plant. With the exception of an increased frequency of abnormal roots of 35S GFP-MBD plants grown on kanamycin-containing media, expression of GFP-MBD does not appear to affect plant phenotype. The number of leaves, branches, bolts, and siliques as well as overall height, leaf size, and seed set are similar between wild-type and transgenic plants as is the rate of root growth. Thus, we conclude that the transgenic plants can serve as a living model system in which the dynamic behavior of microtubules can be visualized. Confocal microscopy was used to simultaneously monitor growth and microtubule behavior within individual cells as they passed through the elongation zone of the Arabidopsis root. Generally, microtubules reoriented from transverse to oblique or longitudinal orientations as growth declined. Microtubule reorientation initiated at the ends of the cell did not necessarily occur simultaneously in adjacent neighboring cells and did not involve complete disintegration and repolymerization of microtubule arrays. Although growth rates correlated with microtubule reorientation, the two processes were not tightly coupled in terms of their temporal relationships, suggesting that other factor(s) may be involved in regulating both events. Additionally, microtubule orientation was more defined in cells whose growth was accelerating and less stringent in cells whose growth was decelerating, indicating that microtubule-orienting factor(s) may be sensitive to growth acceleration, rather than growth per se.

  1. Genome-Resolved Metagenomic Analysis Reveals Roles for Candidate Phyla and Other Microbial Community Members in Biogeochemical Transformations in Oil Reservoirs

    PubMed Central

    Hu, Ping; Tom, Lauren; Singh, Andrea; Thomas, Brian C.; Baker, Brett J.; Piceno, Yvette M.; Andersen, Gary L.

    2016-01-01

    ABSTRACT Oil reservoirs are major sites of methane production and carbon turnover, processes with significant impacts on energy resources and global biogeochemical cycles. We applied a cultivation-independent genomic approach to define microbial community membership and predict roles for specific organisms in biogeochemical transformations in Alaska North Slope oil fields. Produced water samples were collected from six locations between 1,128 m (24 to 27°C) and 2,743 m (80 to 83°C) below the surface. Microbial community complexity decreased with increasing temperature, and the potential to degrade hydrocarbon compounds was most prevalent in the lower-temperature reservoirs. Sulfate availability, rather than sulfate reduction potential, seems to be the limiting factor for sulfide production in some of the reservoirs under investigation. Most microorganisms in the intermediate- and higher-temperature samples were related to previously studied methanogenic and nonmethanogenic archaea and thermophilic bacteria, but one candidate phylum bacterium, a member of the Acetothermia (OP1), was present in Kuparuk sample K3. The greatest numbers of candidate phyla were recovered from the mesothermic reservoir samples SB1 and SB2. We reconstructed a nearly complete genome for an organism from the candidate phylum Parcubacteria (OD1) that was abundant in sample SB1. Consistent with prior findings for members of this lineage, the OD1 genome is small, and metabolic predictions support an obligately anaerobic, fermentation-based lifestyle. At moderate abundance in samples SB1 and SB2 were members of bacteria from other candidate phyla, including Microgenomates (OP11), Atribacteria (OP9), candidate phyla TA06 and WS6, and Marinimicrobia (SAR406). The results presented here elucidate potential roles of organisms in oil reservoir biological processes. PMID:26787827

  2. In Silico Discovery of Potential Uridine-Cytidine Kinase 2 Inhibitors from the Rhizome of Alpinia mutica.

    PubMed

    Malami, Ibrahim; Abdul, Ahmad Bustamam; Abdullah, Rasedee; Bt Kassim, Nur Kartinee; Waziri, Peter; Christopher Etti, Imaobong

    2016-01-01

    Uridine-cytidine kinase 2 is implicated in uncontrolled proliferation of abnormal cells and it is a hallmark of cancer, therefore, there is need for effective inhibitors of this key enzyme. In this study, we employed the used of in silico studies to find effective UCK2 inhibitors of natural origin using bioinformatics tools. An in vitro kinase assay was established by measuring the amount of ADP production in the presence of ATP and 5-fluorouridine as a substrate. Molecular docking studies revealed an interesting ligand interaction with the UCK2 protein for both flavokawain B and alpinetin. Both compounds were found to reduce ADP production, possibly by inhibiting UCK2 activity in vitro. In conclusion, we have identified flavokawain B and alpinetin as potential natural UCK2 inhibitors as determined by their interactions with UCK2 protein using in silico molecular docking studies. This can provide information to identify lead candidates for further drug design and development. PMID:27070566

  3. In Silico Discovery of High Deliverable Capacity Metal-Organic Frameworks

    NASA Astrophysics Data System (ADS)

    Bao, Yi; Martin, Richard; Simon, Cory; Haranczyk, Maciej; Smit, Berend; Deem, Michael; Michael W. Deem Team; Maciej Haranczyk Team; Berend Smit Team

    2015-03-01

    Metal organic frameworks (MOFs) are actively being explored as potential adsorbed natural gas storage materials for small vehicles. Experimental exploration of potential materials is limited by the throughput of synthetic chemistry. We here describe a computational methodology to complement and guide these experimental efforts. The method uses known chemical transformations in silico to identify MOFs with high methane deliverable capacity. The procedure explicitly considers synthesizability with geometric requirements on organic linkers. We efficiently search the composition and conformation space of organic linkers for nine MOF networks, finding 48 materials with higher predicted deliverable capacity (at 65 bar storage, 5.8 bar depletion, and 298 K) than MOF-5 in four of the nine networks. The best material has a predicted deliverable capacity 8% higher than that of MOF-5. US Department of Energy.

  4. Genome-Resolved Metagenomic Analysis Reveals Roles for Candidate Phyla and Other Microbial Community Members in Biogeochemical Transformations in Oil Reservoirs

    DOE PAGESBeta

    Hu, Ping; Tom, Lauren; Singh, Andrea; Thomas, Brian C.; Baker, Brett J.; Piceno, Yvette M.; Andersen, Gary L.; Banfield, Jillian F.

    2016-01-19

    Oil reservoirs are major sites of methane production and carbon turnover, processes with significant impacts on energy resources and global biogeochemical cycles. We applied a cultivation-independent genomic approach to define microbial community membership and predict roles for specific organisms in biogeochemical transformations in Alaska North Slope oil fields. Produced water samples were collected from six locations between 1,128 m (24 to 27°C) and 2,743 m (80 to 83°C) below the surface. Microbial community complexity decreased with increasing temperature, and the potential to degrade hydrocarbon compounds was most prevalent in the lower-temperature reservoirs. Sulfate availability, rather than sulfate reduction potential, seems to bemore » the limiting factor for sulfide production in some of the reservoirs under investigation. Most microorganisms in the intermediate- and higher-temperature samples were related to previously studied methanogenic and nonmethanogenic archaea and thermophilic bacteria, but one candidate phylum bacterium, a member of theAcetothermia(OP1), was present in Kuparuk sample K3. The greatest numbers of candidate phyla were recovered from the mesothermic reservoir samples SB1 and SB2. We reconstructed a nearly complete genome for an organism from the candidate phylumParcubacteria(OD1) that was abundant in sample SB1. Consistent with prior findings for members of this lineage, the OD1 genome is small, and metabolic predictions support an obligately anaerobic, fermentation-based lifestyle. At moderate abundance in samples SB1 and SB2 were members of bacteria from other candidate phyla, includingMicrogenomates(OP11),Atribacteria(OP9), candidate phyla TA06 and WS6, andMarinimicrobia(SAR406). The results presented here elucidate potential roles of organisms in oil reservoir biological processes. The activities of microorganisms in oil reservoirs impact petroleum resource quality and the global carbon cycle. In conclusion, we show that

  5. Deciphering Dimerization Modes of PAS Domains: Computational and Experimental Analyses of the AhR:ARNT Complex Reveal New Insights Into the Mechanisms of AhR Transformation

    PubMed Central

    Corrada, Dario; Soshilov, Anatoly A.; Denison, Michael S.

    2016-01-01

    The Aryl hydrocarbon Receptor (AhR) is a transcription factor that mediates the biochemical response to xenobiotics and the toxic effects of a number of environmental contaminants, including dioxins. Recently, endogenous regulatory roles for the AhR in normal physiology and development have also been reported, thus extending the interest in understanding its molecular mechanisms of activation. Since dimerization with the AhR Nuclear Translocator (ARNT) protein, occurring through the Helix-Loop-Helix (HLH) and PER-ARNT-SIM (PAS) domains, is needed to convert the AhR into its transcriptionally active form, deciphering the AhR:ARNT dimerization mode would provide insights into the mechanisms of AhR transformation. Here we present homology models of the murine AhR:ARNT PAS domain dimer developed using recently available X-ray structures of other bHLH-PAS protein dimers. Due to the different reciprocal orientation and interaction surfaces in the different template dimers, two alternative models were developed for both the PAS-A and PAS-B dimers and they were characterized by combining a number of computational evaluations. Both well-established hot spot prediction methods and new approaches to analyze individual residue and residue-pairwise contributions to the MM-GBSA binding free energies were adopted to predict residues critical for dimer stabilization. On this basis, a mutagenesis strategy for both the murine AhR and ARNT proteins was designed and ligand-dependent DNA binding ability of the AhR:ARNT heterodimer mutants was evaluated. While functional analysis disfavored the HIF2α:ARNT heterodimer-based PAS-B model, most mutants derived from the CLOCK:BMAL1-based AhR:ARNT dimer models of both the PAS-A and the PAS-B dramatically decreased the levels of DNA binding, suggesting this latter model as the most suitable for describing AhR:ARNT dimerization. These novel results open new research directions focused at elucidating basic molecular mechanisms underlying the

  6. Intake and transformation to a glycoside of (Z)-3-hexenol from infested neighbors reveals a mode of plant odor reception and defense

    PubMed Central

    Sugimoto, Koichi; Matsui, Kenji; Iijima, Yoko; Akakabe, Yoshihiko; Muramoto, Shoko; Ozawa, Rika; Uefune, Masayoshi; Sasaki, Ryosuke; Alamgir, Kabir Md.; Akitake, Shota; Nobuke, Tatsunori; Galis, Ivan; Aoki, Koh; Shibata, Daisuke; Takabayashi, Junji

    2014-01-01

    Plants receive volatile compounds emitted by neighboring plants that are infested by herbivores, and consequently the receiver plants begin to defend against forthcoming herbivory. However, to date, how plants receive volatiles and, consequently, how they fortify their defenses, is largely unknown. In this study, we found that undamaged tomato plants exposed to volatiles emitted by conspecifics infested with common cutworms (exposed plants) became more defensive against the larvae than those exposed to volatiles from uninfested conspecifics (control plants) in a constant airflow system under laboratory conditions. Comprehensive metabolite analyses showed that only the amount of (Z)-3-hexenylvicianoside (HexVic) was higher in exposed than control plants. This compound negatively affected the performance of common cutworms when added to an artificial diet. The aglycon of HexVic, (Z)-3-hexenol, was obtained from neighboring infested plants via the air. The amount of jasmonates (JAs) was not higher in exposed plants, and HexVic biosynthesis was independent of JA signaling. The use of (Z)-3-hexenol from neighboring damaged conspecifics for HexVic biosynthesis in exposed plants was also observed in an experimental field, indicating that (Z)-3-hexenol intake occurred even under fluctuating environmental conditions. Specific use of airborne (Z)-3-hexenol to form HexVic in undamaged tomato plants reveals a previously unidentified mechanism of plant defense. PMID:24778218

  7. In silico Testing of Environmental Impact on Embryonic Vascular Development

    EPA Science Inventory

    Understanding risks to embryonic development from exposure to environmental chemicals is a significant challenge given the diverse chemical landscape and paucity of data for most of these compounds. EPA’s Virtual Embryo project is building in silico models of morphogenesis to tes...

  8. In silico models for development of insect repellents

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In silico modeling a common term to describe computer-assisted molecular modeling has been used to make remarkable advances in mechanistic drug design and in the discovery of new potential bioactive chemical entities in recent years. The goal of this chapter will be to focus on new, next-generation ...

  9. Development of a Computational (in silico) Model of Ocular Teratogenesis

    EPA Science Inventory

    EPA’s ToxCast™ project is profiling the in vitro bioactivity of chemical compounds to assess pathway-level and cell-based signatures that are highly correlated with observed in vivo toxicity. In silico models provide a framework for interpreting the in vitro results and for simul...

  10. Editorial: in silico drug design and medicinal chemistry).

    PubMed

    Singla, Rajeev K

    2015-01-01

    Medicinal chemistry is not limited to molecules, their structures and design but also highly cohesive to pharmacological activities. The potency of a molecule varies by its structure. Hence structural activity relationship is the sub-branch which deals with the estimation of ability of a molecule in depicting any pharmacological activity. In silico drug design is a novel technique which is employed in designing a molecule by using computer aided software’s and bringing a superior and potent molecule. In recent years, in silico drug design has been merged with medicinal chemistry especially by the techniques like ligand based strategy to isolate the required structures. By such strategic techniques, there are high chances of delivering high throughput screening which involves of screening large number of molecules in a very less time. Involvement of such techniques would be a boon for development of new drug entity as it can aid in development of newer, safe, effective and potent drug molecules. Hence, the present issue is aimed to emphasize the cohesion between in silico drug design and it significance in medicinal chemistry. The articles which would be published will mainly focus on the role of in silico drug design techniques in the development of molecules to target various disease and disorders. Molecules can from natural/ synthetic/semi synthetic origin. Articles will be a treasure box consisting of employment of computational methods for unprecedented molecules. The issue will be sure an endorsement for international readership and researchers. PMID:25860175

  11. The phase transformation of methane caused by pressure change during its rise from the seafloor revealed by video observation and acoustic reflection data

    NASA Astrophysics Data System (ADS)

    Aoyama, C.

    2013-12-01

    Acoustic reflection depending on physical property differences among solid of methane hydrates and methane gas bubbles from seafloor and sea water.By sending ultrasonic waves from the transducer of an echo sounder or a sonar system through the water and measuring the echo of the back-scatterings from the methane hydrates or bubbles,it is possible that a visualized image of the methane plumes is displayed on the display of an echo sounder or a sonar system.Estimates of the amount of the methane plumes are extremely important for the global environment as part of the carbon cycle.The observations were carried out at Umitaka Spur and Joetsu knoll in the Sea of Japan every year since 2004. There are many methane plumes in the same ocean area. Thus, we investigate minutely about methane plumes in this study.In order to recognize estimates of the methane plumes, we observed the image of methane plumes using a remotely operated submarine vehicle (Hyper Dolphin, of the Japan Agency of Marine-Earth Science and Technology (JAMSTEC)), and captured the methane bubble using a funnel.We observe the images of the methane plumes seeping points on the seafloor taken by a high-definition camera loaded in the vehicle, measure the surfacing velocity of the gushed methane plumes, and compute the surfacing velocity of the gas and solid substance using a theoretical formula.The observation was carried out at Umitaka Spur in the Japan Sea. The depth was 1000 m and the seawater temperature was 0.3 C°.From 3 seeping points, we gathered 300ml of methane in 643 seconds in the funnel with an opening of 20 cm in diameter.If it is assumed that the seeping points are equally scattered in the area, the seeping volume per unit area is 5.4×104cm3 per hour, which is 4.7×102m3 per year.The experiment in the ocean revealed the followings.The methane hydrate particles that are seeping out from seafloor are solid substances just above the seafloor.In the studied ocean area, 7.7×104m3 of methane

  12. In-Silico Computing of the Most Deleterious nsSNPs in HBA1 Gene

    PubMed Central

    AbdulAzeez, Sayed; Borgio, J. Francis

    2016-01-01

    Background α-Thalassemia (α-thal) is a genetic disorder caused by the substitution of single amino acid or large deletions in the HBA1 and/or HBA2 genes. Method Using modern bioinformatics tools as a systematic in-silico approach to predict the deleterious SNPs in the HBA1 gene and its significant pathogenic impact on the functions and structure of HBA1 protein was predicted. Results and Discussion A total of 389 SNPs in HBA1 were retrieved from dbSNP database, which includes: 201 non-coding synonymous (nsSNPs), 43 human active SNPs, 16 intronic SNPs, 11 mRNA 3′ UTR SNPs, 9 coding synonymous SNPs, 9 5′ UTR SNPs and other types. Structural homology-based method (PolyPhen) and sequence homology-based tool (SIFT), SNPs&Go, PROVEAN and PANTHER revealed that 2.4% of the nsSNPs are pathogenic. Conclusions A total of 5 nsSNPs (G60V, K17M, K17T, L92F and W15R) were predicted to be responsible for the structural and functional modifications of HBA1 protein. It is evident from the deep comprehensive in-silico analysis that, two nsSNPs such as G60Vand W15R in HBA1 are highly deleterious. These “2 pathogenic nsSNPs” can be considered for wet-lab confirmatory analysis. PMID:26824843

  13. Integrated molecular, physiological and in silico characterization of two Halomonas isolates from industrial brine.

    PubMed

    Carlson, Ross P; Oshota, Olusegun; Shipman, Matt; Caserta, Justin A; Hu, Ping; Saunders, Charles W; Xu, Jun; Jay, Zackary J; Reeder, Nancy; Richards, Abigail; Pettigrew, Charles; Peyton, Brent M

    2016-05-01

    Two haloalkaliphilic bacteria isolated from industrial brine solutions were characterized via molecular, physiological, and in silico metabolic pathway analyses. Genomes from the organisms, designated Halomonas BC1 and BC2, were sequenced; 16S ribosomal subunit-based phylogenetic analysis revealed a high level of similarity to each other and to Halomonas meridiana. Both strains were moderate halophiles with near optimal specific growth rates (≥60 % μ max) observed over <0.1-5 % (w/v) NaCl and pH ranging from 7.4 to 10.2. Isolate BC1 was further characterized by measuring uptake or synthesis of compatible solutes under different growth conditions; in complex medium, uptake and accumulation of external glycine betaine was observed while ectoine was synthesized de novo in salts medium. Transcriptome analysis of isolate BC1 grown on glucose or citrate medium measured differences in glycolysis- and gluconeogenesis-based metabolisms, respectively. The annotated BC1 genome was used to build an in silico, genome-scale stoichiometric metabolic model to study catabolic energy strategies and compatible solute synthesis under gradients of oxygen and nutrient availability. The theoretical analysis identified energy metabolism challenges associated with acclimation to high salinity and high pH. The study documents central metabolism data for the industrially and scientifically important haloalkaliphile genus Halomonas. PMID:26888357

  14. Predicting In Vivo Responses to Biomaterials via Combined In Vitro and In Silico Analysis

    PubMed Central

    Wolf, Matthew T.; Vodovotz, Yoram; Tottey, Stephen; Brown, Bryan N.

    2015-01-01

    The host response to both synthetic and biologically derived biomaterials is a temporally regulated, complex process that involves multiple interacting cell types. This complexity has classically limited the efficacy of in vitro assays for predicting the in vivo outcome, necessitating the use of costly animal models for biomaterial development. The present study addressed these challenges by developing an in vitro assay that characterized the dynamic inflammatory response of human monocyte-derived-macrophages to biomaterials, coupled with quasi-mechanistic analysis in silico analysis: principal component analysis (PCA) and dynamic network analysis (DyNA). Synthetic and extracellular matrix (ECM)–derived materials were evaluated using this method, and were then associated with the in vivo remodeling and macrophage polarization response in a rodent skeletal muscle injury model. PCA and DyNA revealed a distinct in vitro macrophage response to ECM materials that corresponded to constructive remodeling and an increased M2 macrophage presence in vivo. In contrast, PCA and DyNA suggested a response to crosslinked ECM and synthetic materials characteristic of a foreign body reaction and dominant M1 macrophage response. These results suggest that in silico analysis of an in vitro macrophage assay may be useful as a predictor for determining the in vivo host response to implanted biomaterials. PMID:24980950

  15. Fumaric Acid Production in Saccharomyces cerevisiae by In Silico Aided Metabolic Engineering

    PubMed Central

    Xu, Guoqiang; Zou, Wei; Chen, Xiulai; Xu, Nan; Liu, Liming; Chen, Jian

    2012-01-01

    Fumaric acid (FA) is a promising biomass-derived building-block chemical. Bio-based FA production from renewable feedstock is a promising and sustainable alternative to petroleum-based chemical synthesis. Here we report on FA production by direct fermentation using metabolically engineered Saccharomyces cerevisiae with the aid of in silico analysis of a genome-scale metabolic model. First, FUM1 was selected as the target gene on the basis of extensive literature mining. Flux balance analysis (FBA) revealed that FUM1 deletion can lead to FA production and slightly lower growth of S. cerevisiae. The engineered S. cerevisiae strain obtained by deleting FUM1 can produce FA up to a concentration of 610±31 mg L–1 without any apparent change in growth in fed-batch culture. FT-IR and 1H and 13C NMR spectra confirmed that FA was synthesized by the engineered S. cerevisiae strain. FBA identified pyruvate carboxylase as one of the factors limiting higher FA production. When the RoPYC gene was introduced, S. cerevisiae produced 1134±48 mg L–1 FA. Furthermore, the final engineered S. cerevisiae strain was able to produce 1675±52 mg L–1 FA in batch culture when the SFC1 gene encoding a succinate–fumarate transporter was introduced. These results demonstrate that the model shows great predictive capability for metabolic engineering. Moreover, FA production in S. cerevisiae can be efficiently developed with the aid of in silico metabolic engineering. PMID:23300594

  16. Identification of novel bacterial DNA gyrase inhibitors: An in silico study

    PubMed Central

    Rahimi, Hamzeh; Najafi, Ali; Eslami, Habib; Negahdari, Babak; Moghaddam, Mehrdad Moosazadeh

    2016-01-01

    Owing to essential role in bacterial survival, DNA gyrase has been exploited as a validated drug target. However, rapidly emerging resistance to gyrase-targeted drugs such as widely utilized fluoroquinolones reveals the necessity to develop novel compounds with new mechanism of actions against this enzyme. Here, an attempt has been made to identify new drug-like molecules for Shigella flexneri DNA gyrase inhibition through in silico approaches. The structural similarity search was carried out using the natural product simocyclinone D8, a unique gyrase inhibitor, to virtually screen ZINC database. A total of 11830 retrieved hits were further screened for selection of high-affinity compounds by implementing molecular docking followed by investigation of druggability according to Lipinski’s rule, biological activity and physiochemical properties. Among the hits initially identified, three molecules were then confirmed to have reasonable gyrase-binding affinity and to follow Lipinski’s rule. Based on these in silico findings, three compounds with different chemical structures from previously identified gyrase inhibitors were proposed as potential candidates for the treatment of fluoroquinolone-resistant strains and deserve further investigations. PMID:27499795

  17. In Silico Characterization of Functional Divergence of Two Cathelicidin Variants in Indian Sheep

    PubMed Central

    Dhaliwal, Kamaljeet K; Arora, Jaspreet S; Mukhopadhyay, Chandra S; Dubey, Prem P

    2015-01-01

    The present work focuses on the in silico characterization of functional divergence of two ovine cathelicidin coding sequence (cds) variants (ie, Cath1 and Cath2) of Indian sheep. Overlapping partial cds of both the cathelicidin variants were cloned in pJet1.2/blunt vector and sequenced. Evolutionary analysis of the Cath2 and Cath1 indicated that the mammalian cathelicidins clustered separately from avian fowlicidins. The avian fowlicidins, which are very different from mammalian cathelicidins (Caths), clearly displayed signatures of purifying selection. The pairwise sequence alignments of translated amino acid sequences of these two sheep cathelicidins showed gaps in the antimicrobial domain of Cath1 variant; however, the amino terminal cathelin regions of both the Caths were conserved. Amino acid sequence analysis of full-length cathelicidins available at public database revealed that Cath1, Cath2, and Cath7 of different ruminant species (including our Cath1 and Cath2 variants) formed individual clads, suggesting that these types have evolved to target specific types of microbes. In silico analysis of Cath1 and Cath2 peptide sequences indicated that the C-terminal antimicrobial peptide domain of Cath2 is more immunogenic than that of the ovine Cath1 due to its higher positive antigenic index, making Cath1 a promising antigen for production of monoclonal antibodies. PMID:26380546

  18. Identification of novel bacterial DNA gyrase inhibitors: An in silico study.

    PubMed

    Rahimi, Hamzeh; Najafi, Ali; Eslami, Habib; Negahdari, Babak; Moghaddam, Mehrdad Moosazadeh

    2016-01-01

    Owing to essential role in bacterial survival, DNA gyrase has been exploited as a validated drug target. However, rapidly emerging resistance to gyrase-targeted drugs such as widely utilized fluoroquinolones reveals the necessity to develop novel compounds with new mechanism of actions against this enzyme. Here, an attempt has been made to identify new drug-like molecules for Shigella flexneri DNA gyrase inhibition through in silico approaches. The structural similarity search was carried out using the natural product simocyclinone D8, a unique gyrase inhibitor, to virtually screen ZINC database. A total of 11830 retrieved hits were further screened for selection of high-affinity compounds by implementing molecular docking followed by investigation of druggability according to Lipinski's rule, biological activity and physiochemical properties. Among the hits initially identified, three molecules were then confirmed to have reasonable gyrase-binding affinity and to follow Lipinski's rule. Based on these in silico findings, three compounds with different chemical structures from previously identified gyrase inhibitors were proposed as potential candidates for the treatment of fluoroquinolone-resistant strains and deserve further investigations. PMID:27499795

  19. From Structure and Function of Proteins Toward in Silico Biology

    NASA Astrophysics Data System (ADS)

    Yamato, Ichiro

    2013-01-01

    Researches of biology are targeted on three major flows, materials (or chemicals), energy, and information. I have been mainly concerned with the studies on bioenergy transducing mechanisms. I have studied the mechanism of secondary active transport systems and proposed an affinity change mechanism as a general hypothesis, then tried to confirm that it is applicable to other kinds of bioenergy transducing systems. Choosing Na+-translocating V-type ATPase from Enterococcus hirae as target, I hypothesized the affinity change mechanism for the energy transduction of this ATPase. Here I describe several three dimensional structures of parts of the ATPase supporting my hypothesis. From such detailed and extensive researches on protein structure/function relationship, we can proceed toward the in silico biology, which I described previously in 2007 ([1] "Toward in silico biology").

  20. Mobile genetic elements: in silico, in vitro, in vivo.

    PubMed

    Arkhipova, Irina R; Rice, Phoebe A

    2016-03-01

    Mobile genetic elements (MGEs), also called transposable elements (TEs), represent universal components of most genomes and are intimately involved in nearly all aspects of genome organization, function and evolution. However, there is currently a gap between the fast pace of TE discovery in silico, driven by the exponential growth of comparative genomic studies, and a limited number of experimental models amenable to more traditional in vitro and in vivo studies of structural, mechanistic and regulatory properties of diverse MGEs. Experimental and computational scientists came together to bridge this gap at a recent conference, 'Mobile Genetic Elements: in silico, in vitro, in vivo', held at the Marine Biological Laboratory (MBL) in Woods Hole, MA, USA. PMID:26822117

  1. Evaluation of a Genome-Scale In Silico Metabolic Model for Geobacter metallireducens Using Proteomic Data from a Field Biostimulation Experiment

    SciTech Connect

    Fang, Yilin; Wilkins, Michael J.; Yabusaki, Steven B.; Lipton, Mary S.; Long, Philip E.

    2012-12-12

    Biomass and shotgun global proteomics data that reflected relative protein abundances from samples collected during the 2008 experiment at the U.S. Department of Energy Integrated Field-Scale Subsurface Research Challenge site in Rifle, Colorado, provided an unprecedented opportunity to validate a genome-scale metabolic model of Geobacter metallireducens and assess its performance with respect to prediction of metal reduction, biomass yield, and growth rate under dynamic field conditions. Reconstructed from annotated genomic sequence, biochemical, and physiological data, the constraint-based in silico model of G. metallireducens relates an annotated genome sequence to the physiological functions with 697 reactions controlled by 747 enzyme-coding genes. Proteomic analysis showed that 180 of the 637 G. metallireducens proteins detected during the 2008 experiment were associated with specific metabolic reactions in the in silico model. When the field-calibrated Fe(III) terminal electron acceptor process reaction in a reactive transport model for the field experiments was replaced with the genome-scale model, the model predicted that the largest metabolic fluxes through the in silico model reactions generally correspond to the highest abundances of proteins that catalyze those reactions. Central metabolism predicted by the model agrees well with protein abundance profiles inferred from proteomic analysis. Model discrepancies with the proteomic data, such as the relatively low fluxes through amino acid transport and metabolism, revealed pathways or flux constraints in the in silico model that could be updated to more accurately predict metabolic processes that occur in the subsurface environment.

  2. Reveal Protein Molecular Structural-Chemical Differrences Between Two Types of Winterfat (Forage) Seeds with Physiological Differences in Low Temperature Tolerance Using Synchrotron-Based Fourier Transform Infrared Microspectroscopy

    SciTech Connect

    Yu,P.; Wang, R.; Bai, Y.

    2005-01-01

    Winterfat (Krascheninnikovia lanata) (forage seed) is a long-lived native shrub with superior forage quality for livestock and wildlife. The objectives of this study were to use advanced synchrotron technology [S-Fourier transform infrared microspectroscopy (FTIR)] as a novel approach to reveal protein molecular structural-chemical differences in terms of protein secondary structures between the two types of winterfat (forage) seeds, which show physiological differences in low-temperature tolerances. This experiment was performed at beamline U10B at the National Synchrotron Light Source NSLS in Brookhaven National Laboratory BNL, U.S. Department of Energy (NSLS-BNL, New York). The results showed that with the synchrotron analytical technique (S-FTIR), the molecular structural-chemical makeup and characteristics of the winterfat seed tissues could be imaged and revealed. The protein secondary structures differed between the large and the small seed tissues. By using the multicomponent peaks modeling method, the results show that the large seeds contained no significant differences (P > 0.05) in percentage of {beta}-sheet (average 37.0%) and {alpha}-helix (average 24.1%). However, the large seeds contained a lower (P < 0.05) percentage of {beta}-turns (18.1 vs. 20.1%) and a lower (P < 0.05) ratio of {beta}-turns to {alpha}-helices (0.8 vs. 0.9) and {beta}-turns to {beta}-sheets (0.5 vs. 0.6). Our results demonstrate the potential of highly spatially resolved synchrotron-based FTIR microspectroscopy to reveal differences of structural molecular chemistry and protein secondary structures, which are associated with seed size variation and may affect germination behaviors.

  3. In silico ADME/T modelling for rational drug design.

    PubMed

    Wang, Yulan; Xing, Jing; Xu, Yuan; Zhou, Nannan; Peng, Jianlong; Xiong, Zhaoping; Liu, Xian; Luo, Xiaomin; Luo, Cheng; Chen, Kaixian; Zheng, Mingyue; Jiang, Hualiang

    2015-11-01

    In recent decades, in silico absorption, distribution, metabolism, excretion (ADME), and toxicity (T) modelling as a tool for rational drug design has received considerable attention from pharmaceutical scientists, and various ADME/T-related prediction models have been reported. The high-throughput and low-cost nature of these models permits a more streamlined drug development process in which the identification of hits or their structural optimization can be guided based on a parallel investigation of bioavailability and safety, along with activity. However, the effectiveness of these tools is highly dependent on their capacity to cope with needs at different stages, e.g. their use in candidate selection has been limited due to their lack of the required predictability. For some events or endpoints involving more complex mechanisms, the current in silico approaches still need further improvement. In this review, we will briefly introduce the development of in silico models for some physicochemical parameters, ADME properties and toxicity evaluation, with an emphasis on the modelling approaches thereof, their application in drug discovery, and the potential merits or deficiencies of these models. Finally, the outlook for future ADME/T modelling based on big data analysis and systems sciences will be discussed. PMID:26328949

  4. Predicting pharmacokinetic profiles using in silico derived parameters.

    PubMed

    Hosea, Natalie A; Jones, Hannah M

    2013-04-01

    Human pharmacokinetic (PK) predictions play a critical role in assessing the quality of potential clinical candidates where the accurate estimation of clearance, volume of distribution, bioavailability, and the plasma-concentration-time profiles are the desired end points. While many methods for conducting predictions utilize in vivo data, predictions can be conducted successfully from in vitro or in silico data, applying modeling and simulation techniques. This approach can be facilitated using commercially available prediction software such as GastroPlus which has been reported to accurately predict the oral PK profile of small drug-like molecules. Herein, case studies are described where GastroPlus modeling and simulation was employed using in silico or in vitro data to predict PK profiles in early discovery. The results obtained demonstrate the feasibility of adequately predicting plasma-concentration-time profiles with in silico derived as well as in vitro measured parameters and hence predicting PK profiles with minimal data. The applicability of this approach can provide key information enabling decisions on either dose selection, chemistry strategy to improve compounds, or clinical protocol design, thus demonstrating the value of modeling and simulation in both early discovery and exploratory development for predicting absorption and disposition profiles. PMID:23427934

  5. AutoClickChem: Click Chemistry in Silico

    PubMed Central

    Durrant, Jacob D.; McCammon, J. Andrew

    2012-01-01

    Academic researchers and many in industry often lack the financial resources available to scientists working in “big pharma.” High costs include those associated with high-throughput screening and chemical synthesis. In order to address these challenges, many researchers have in part turned to alternate methodologies. Virtual screening, for example, often substitutes for high-throughput screening, and click chemistry ensures that chemical synthesis is fast, cheap, and comparatively easy. Though both in silico screening and click chemistry seek to make drug discovery more feasible, it is not yet routine to couple these two methodologies. We here present a novel computer algorithm, called AutoClickChem, capable of performing many click-chemistry reactions in silico. AutoClickChem can be used to produce large combinatorial libraries of compound models for use in virtual screens. As the compounds of these libraries are constructed according to the reactions of click chemistry, they can be easily synthesized for subsequent testing in biochemical assays. Additionally, in silico modeling of click-chemistry products may prove useful in rational drug design and drug optimization. AutoClickChem is based on the pymolecule toolbox, a framework that may facilitate the development of future python-based programs that require the manipulation of molecular models. Both the pymolecule toolbox and AutoClickChem are released under the GNU General Public License version 3 and are available for download from http://autoclickchem.ucsd.edu. PMID:22438795

  6. In silico and in vivo studies of an Arabidopsis thaliana gene, ACR2, putatively involved in arsenic accumulation in plants.

    PubMed

    Nahar, Noor; Rahman, Aminur; Moś, Maria; Warzecha, Tomasz; Algerin, Maria; Ghosh, Sibdas; Johnson-Brousseau, Sheila; Mandal, Abul

    2012-09-01

    Previously, our in silico analyses identified four candidate genes that might be involved in uptake and/or accumulation of arsenics in plants: arsenate reductase 2 (ACR2), phytochelatin synthase 1 (PCS1) and two multi-drug resistant proteins (MRP1 and MRP2) [Lund et al. (2010) J Biol Syst 18:223-224]. We also postulated that one of these four genes, ACR2, seems to play a central role in this process. To investigate further, we have constructed a 3D structure of the Arabidopsis thaliana ACR2 protein using the iterative implementation of the threading assembly refinement (I-TASSER) server. These analyses revealed that, for catalytic metabolism of arsenate, the arsenate binding-loop (AB-loop) and residues Phe-53, Phe-54, Cys-134, Cys-136, Cys-141, Cys-145, and Lys-135 are essential for reducing arsenate to arsenic intermediates (arsenylated enzyme-substrate intermediates) and arsenite in plants. Thus, functional predictions suggest that the ACR2 protein is involved in the conversion of arsenate to arsenite in plant cells. To validate the in silico results, we exposed a transfer-DNA (T-DNA)-tagged mutant of A. thaliana (mutation in the ACR2 gene) to various amounts of arsenic. Reverse transcriptase PCR revealed that the mutant exhibits significantly reduced expression of the ACR2 gene. Spectrophotometric analyses revealed that the amount of accumulated arsenic compounds in this mutant was approximately six times higher than that observed in control plants. The results obtained from in silico analyses are in complete agreement with those obtained in laboratory experiments. PMID:22562211

  7. Evidence for the conformational rigidity of triplex d(C +T) 8-d(AG) 8·d(CT) 8 on silver electrode revealed by Fourier transform Raman scattering studies

    NASA Astrophysics Data System (ADS)

    Fang, Ye; Bai, Chunli; Wang, Ting; Zhong, Faping; Tang, Youqi; Lin, S. B.; Kan, Lou-sing

    1996-03-01

    Fourier transform surface enhanced Raman scattering spectroscopy (FT-SERS) has been first applied to characterize the triple stranded helix d(C +T) 8-d(AG) 8·d(CT) 8 (pH 4.5) (triplex) and its corresponding double-stranded helix d(AG) 8·d(CT) 8 (pH 7.0) (duplex) at an ex situ roughened silver electrode polarized at between 0.0 and -1.0 V vs. {Ag}/{AgCl}. The triplex adsorbed on the silver electrode yields five intense and one weak SERS bands located at 241, 839, 1189, 1293, 1643, and 1530 cm -1, respectively. These bands are not seen in the FT-SERS spectrum of the duplex, which showed a pattern similar to that of an oligo-DNA duplex observed by Koglin and Sequaries (Top. Curr. Chem., 134 (1989) 1). In the case of the triplex, the occurrence of the 839 cm -1 band with concomitant disappearance of the adsorbed adenine ring-breathing band at 734 cm -1 of the duplex indicates that the helical structure of the triplex near the surface of the silver electrode is well preserved and exhibits conformational rigidity. We observed a desorption process of the triplex from the silver electrode when the electrode approached -0.9 V (potential of zero charge of the triplex) vs. {Ag}/{AgCl}. This indicates that the highly negatively charged triplex shows a more favorable absorption on a highly positively charged silver surface. The structure of the triplex has also been studied by Fourier transform infrared (FTIR) and Raman spectroscopy. The vibrational spectra obtained clearly revealed that the conformation of the sugar moiety of the purine strand and one pyrimidine strand in the triplex is C 2'-endo/anti, whereas that of the other pyrimidine strand is C 3'-endo/anti.

  8. Whole Exome Sequencing Reveals Novel PHEX Splice Site Mutations in Patients with Hypophosphatemic Rickets

    PubMed Central

    Gillies, Christopher; Sampson, Matthew G.; Kher, Vijay; Sethi, Sidharth K.; Otto, Edgar A.

    2015-01-01

    Objective Hypophosphatemic rickets (HR) is a heterogeneous genetic phosphate wasting disorder. The disease is most commonly caused by mutations in the PHEX gene located on the X-chromosome or by mutations in CLCN5, DMP1, ENPP1, FGF23, and SLC34A3. The aims of this study were to perform molecular diagnostics for four patients with HR of Indian origin (two independent families) and to describe their clinical features. Methods We performed whole exome sequencing (WES) for the affected mother of two boys who also displayed the typical features of HR, including bone malformations and phosphate wasting. B-lymphoblast cell lines were established by EBV transformation and subsequent RT-PCR to investigate an uncommon splice site variant found by WES. An in silico analysis was done to obtain accurate nucleotide frequency occurrences of consensus splice positions other than the canonical sites of all human exons. Additionally, we applied direct Sanger sequencing for all exons and exon/intron boundaries of the PHEX gene for an affected girl from an independent second Indian family. Results WES revealed a novel PHEX splice acceptor mutation in intron 9 (c.1080-3C>A) in a family with 3 affected individuals with HR. The effect on splicing of this mutation was further investigated by RT-PCR using RNA obtained from a patient’s EBV-transformed lymphoblast cell line. RT-PCR revealed an aberrant splice transcript skipping exons 10-14 which was not observed in control samples, confirming the diagnosis of X-linked dominant hypophosphatemia (XLH). The in silico analysis of all human splice sites adjacent to all 327,293 exons across 81,814 transcripts among 20,345 human genes revealed that cytosine is, with 64.3%, the most frequent nucleobase at the minus 3 splice acceptor position, followed by thymidine with 28.7%, adenine with 6.3%, and guanine with 0.8%. We generated frequency tables and pictograms for the extended donor and acceptor splice consensus regions by analyzing all human

  9. In silico and in vitro analysis of rare germline allelic variants of RET oncogene associated with medullary thyroid cancer.

    PubMed

    Cosci, B; Vivaldi, A; Romei, C; Gemignani, F; Landi, S; Ciampi, R; Tacito, A; Molinaro, E; Agate, L; Bottici, V; Cappagli, V; Viola, D; Piaggi, P; Vitti, P; Pinchera, A; Elisei, R

    2011-10-01

    Germline and somatic RET oncogene mutations are found in 98% hereditary and 40% sporadic medullary thyroid carcinomas. Our aim was to analyse by in silico and in vitro assays the transforming activity of six rare RET mutations (T338I, V648I, M918V, A883T, S904F and M848T). Six known RET mutations were used as controls. The in silico analysis showed the highest score value (i.e. 65) for S904F, M848T, M918T and C634R, whereas L790F, G691S, T338I and V648I had 0 score. Intermediate score values were obtained by A883T (score=55), M918V, V804M and Y791F (score=15). The in vitro focus formation assay showed that cells transfected with S904F, M918T, M848T or C634R generated the largest number of focus formation units (FFU). Intermediate numbers of FFU were observed in cells transfected with M918V, V804M, Y791F or A883T, while cells transfected with L790F, G691S, T338I or V648I showed a number of FFU similar to control cells. A positive correlation between the in silico score and in vitro FFU was found (P=0.0005). Only cells transfected with M918T or C634R grew faster and generated higher number of colonies in soft agar than control cells. However, the cells that were transfected with V804M produced an intermediate number of colonies. In conclusion, two of the six rare RET mutations, S904F and M848T possessed a relatively high transforming activity but a low aggressiveness; the other four mutations T338I, V648I, M918V and A883T were low or non-transforming, and their ability to induce tumoural transformation might be related to particular genetic conditions. PMID:21810974

  10. Evaluation of a Genome-Scale In Silico Metabolic Model for Geobacter metallireducens by Using Proteomic Data from a Field Biostimulation Experiment

    PubMed Central

    Fang, Yilin; Yabusaki, Steven B.; Lipton, Mary S.; Long, Philip E.

    2012-01-01

    Accurately predicting the interactions between microbial metabolism and the physical subsurface environment is necessary to enhance subsurface energy development, soil and groundwater cleanup, and carbon management. This study was an initial attempt to confirm the metabolic functional roles within an in silico model using environmental proteomic data collected during field experiments. Shotgun global proteomics data collected during a subsurface biostimulation experiment were used to validate a genome-scale metabolic model of Geobacter metallireducens—specifically, the ability of the metabolic model to predict metal reduction, biomass yield, and growth rate under dynamic field conditions. The constraint-based in silico model of G. metallireducens relates an annotated genome sequence to the physiological functions with 697 reactions controlled by 747 enzyme-coding genes. Proteomic analysis showed that 180 of the 637 G. metallireducens proteins detected during the 2008 experiment were associated with specific metabolic reactions in the in silico model. When the field-calibrated Fe(III) terminal electron acceptor process reaction in a reactive transport model for the field experiments was replaced with the genome-scale model, the model predicted that the largest metabolic fluxes through the in silico model reactions generally correspond to the highest abundances of proteins that catalyze those reactions. Central metabolism predicted by the model agrees well with protein abundance profiles inferred from proteomic analysis. Model discrepancies with the proteomic data, such as the relatively low abundances of proteins associated with amino acid transport and metabolism, revealed pathways or flux constraints in the in silico model that could be updated to more accurately predict metabolic processes that occur in the subsurface environment. PMID:23042184

  11. Analytical workflow of double-digest restriction site-associated DNA sequencing based on empirical and in silico optimization in tomato.

    PubMed

    Shirasawa, Kenta; Hirakawa, Hideki; Isobe, Sachiko

    2016-04-01

    Double-digest restriction site-associated DNA sequencing (ddRAD-Seq) enables high-throughput genome-wide genotyping with next-generation sequencing technology. Consequently, this method has become popular in plant genetics and breeding. Although computational in silico prediction of restriction sites from the genome sequence is recognized as an effective approach for choosing the restriction enzymes to be used, few reports have evaluated the in silico predictions in actual experimental data. In this study, we designed and demonstrated a workflow for in silico and empirical ddRAD-Seq analysis in tomato, as follows: (i)in silico prediction of optimum restriction enzymes from the reference genome, (ii) verification of the prediction by actual ddRAD-Seq data of four restriction enzyme combinations, (iii) establishment of a computational data processing pipeline for high-confidence single nucleotide polymorphism (SNP) calling, and (iv) validation of SNP accuracy by construction of genetic linkage maps. The quality of SNPs based on de novo assembly reference of the ddRAD-Seq reads was comparable with that of SNPs obtained using the published reference genome of tomato. Comparisons of SNP calls in diverse tomato lines revealed that SNP density in the genome influenced the detectability of SNPs by ddRAD-Seq. In silico prediction prior to actual analysis contributed to optimization of the experimental conditions for ddRAD-Seq, e.g. choices of enzymes and plant materials. Following optimization, this ddRAD-Seq pipeline could help accelerate genetics, genomics, and molecular breeding in both model and non-model plants, including crops. PMID:26932983

  12. Analytical workflow of double-digest restriction site-associated DNA sequencing based on empirical and in silico optimization in tomato

    PubMed Central

    Shirasawa, Kenta; Hirakawa, Hideki; Isobe, Sachiko

    2016-01-01

    Double-digest restriction site-associated DNA sequencing (ddRAD-Seq) enables high-throughput genome-wide genotyping with next-generation sequencing technology. Consequently, this method has become popular in plant genetics and breeding. Although computational in silico prediction of restriction sites from the genome sequence is recognized as an effective approach for choosing the restriction enzymes to be used, few reports have evaluated the in silico predictions in actual experimental data. In this study, we designed and demonstrated a workflow for in silico and empirical ddRAD-Seq analysis in tomato, as follows: (i) in silico prediction of optimum restriction enzymes from the reference genome, (ii) verification of the prediction by actual ddRAD-Seq data of four restriction enzyme combinations, (iii) establishment of a computational data processing pipeline for high-confidence single nucleotide polymorphism (SNP) calling, and (iv) validation of SNP accuracy by construction of genetic linkage maps. The quality of SNPs based on de novo assembly reference of the ddRAD-Seq reads was comparable with that of SNPs obtained using the published reference genome of tomato. Comparisons of SNP calls in diverse tomato lines revealed that SNP density in the genome influenced the detectability of SNPs by ddRAD-Seq. In silico prediction prior to actual analysis contributed to optimization of the experimental conditions for ddRAD-Seq, e.g. choices of enzymes and plant materials. Following optimization, this ddRAD-Seq pipeline could help accelerate genetics, genomics, and molecular breeding in both model and non-model plants, including crops. PMID:26932983

  13. In silico Target Fishing for Rationalized Ligand Discovery Exemplified on Constituents of Ruta graveolens

    PubMed Central

    Rollinger, Judith M.; Schuster, Daniela; Danzl, Birgit; Schwaiger, Stefan; Markt, Patrick; Schmidtke, Michaela; Gertsch, Jürg; Raduner, Stefan; Wolber, Gerhard; Langer, Thierry; Stuppner, Hermann

    2012-01-01

    The identification of targets whose interaction is likely to result in the successful treatment of a disease is of growing interest for natural product scientists. In the current study we performed an exemplary application of a virtual parallel screening approach to identify potential targets for 16 secondary metabolites isolated and identified from the aerial parts of the medicinal plant Ruta graveolens L. Low energy conformers of the isolated constituents were simultaneously screened against a set of 2208 pharmacophore models generated in-house for the in silico prediction of putative biological targets, i. e., target fishing. Based on the predicted ligand-target interactions, we focused on three biological targets, namely acetylcholinesterase (AChE), the human rhinovirus (HRV) coat protein and the cannabinoid receptor type-2 (CB2). For a critical evaluation of the applied parallel screening approach, virtual hits and non-hits were assayed on the respective targets. For AChE the highest scoring virtual hit, arborinine, showed the best inhibitory in vitro activity on AChE (IC50 34.7 μM). Determination of the anti-HRV-2 effect revealed 6,7,8-trimethoxycoumarin and arborinine to be the most active antiviral constituents with IC50 values of 11.98 μM and 3.19 μM, respectively. Of these, arborinine was predicted virtually. Of all the molecules subjected to parallel screening, one virtual CB2 ligand was obtained, i.e., rutamarin. Interestingly, in experimental studies only this compound showed a selective activity to the CB2 receptor (Ki of 7.4 μM) by using a radioligand displacement assay. The applied parallel screening paradigm with constituents of R. graveolens on three different proteins has shown promise as an in silico tool for rational target fishing and pharmacological profiling of extracts and single chemical entities in natural product research. PMID:19096995

  14. Dietary Flaxseed Mitigates Impaired Skeletal Muscle Regeneration: in Vivo, in Vitro and in Silico Studies

    PubMed Central

    Carotenuto, Felicia; Costa, Alessandra; Albertini, Maria Cristina; Rocchi, Marco Bruno Luigi; Rudov, Alexander; Coletti, Dario; Minieri, Marilena; Di Nardo, Paolo; Teodori, Laura

    2016-01-01

    Background: Diets enriched with n-3 polyunsaturated fatty acids (n-3 PUFAs) have been shown to exert a positive impact on muscle diseases. Flaxseed is one of the richest sources of n-3 PUFA acid α-linolenic acid (ALA). The aim of this study was to assess the effects of flaxseed and ALA in models of skeletal muscle degeneration characterized by high levels of Tumor Necrosis Factor-α (TNF). Methods: The in vivo studies were carried out on dystrophic hamsters affected by muscle damage associated with high TNF plasma levels and fed with a long-term 30% flaxseed-supplemented diet. Differentiating C2C12 myoblasts treated with TNF and challenged with ALA represented the in vitro model. Skeletal muscle morphology was scrutinized by applying the Principal Component Analysis statistical method. Apoptosis, inflammation and myogenesis were analyzed by immunofluorescence. Finally, an in silico analysis was carried out to predict the possible pathways underlying the effects of n-3 PUFAs. Results: The flaxseed-enriched diet protected the dystrophic muscle from apoptosis and preserved muscle myogenesis by increasing the myogenin and alpha myosin heavy chain. Moreover, it restored the normal expression pattern of caveolin-3 thereby allowing protein retention at the sarcolemma. ALA reduced TNF-induced apoptosis in differentiating myoblasts and prevented the TNF-induced inhibition of myogenesis, as demonstrated by the increased expression of myogenin, myosin heavy chain and caveolin-3, while promoting myotube fusion. The in silico investigation revealed that FAK pathways may play a central role in the protective effects of ALA on myogenesis. Conclusions: These findings indicate that flaxseed may exert potent beneficial effects by preserving skeletal muscle regeneration and homeostasis partly through an ALA-mediated action. Thus, dietary flaxseed and ALA may serve as a useful strategy for treating patients with muscle dystrophies. PMID:26941581

  15. Tubulin Bond Energies and Microtubule Biomechanics Determined from Nanoindentation in Silico

    PubMed Central

    2015-01-01

    Microtubules, the primary components of the chromosome segregation machinery, are stabilized by longitudinal and lateral noncovalent bonds between the tubulin subunits. However, the thermodynamics of these bonds and the microtubule physicochemical properties are poorly understood. Here, we explore the biomechanics of microtubule polymers using multiscale computational modeling and nanoindentations in silico of a contiguous microtubule fragment. A close match between the simulated and experimental force–deformation spectra enabled us to correlate the microtubule biomechanics with dynamic structural transitions at the nanoscale. Our mechanical testing revealed that the compressed MT behaves as a system of rigid elements interconnected through a network of lateral and longitudinal elastic bonds. The initial regime of continuous elastic deformation of the microtubule is followed by the transition regime, during which the microtubule lattice undergoes discrete structural changes, which include first the reversible dissociation of lateral bonds followed by irreversible dissociation of the longitudinal bonds. We have determined the free energies of dissociation of the lateral (6.9 ± 0.4 kcal/mol) and longitudinal (14.9 ± 1.5 kcal/mol) tubulin–tubulin bonds. These values in conjunction with the large flexural rigidity of tubulin protofilaments obtained (18,000–26,000 pN·nm2) support the idea that the disassembling microtubule is capable of generating a large mechanical force to move chromosomes during cell division. Our computational modeling offers a comprehensive quantitative platform to link molecular tubulin characteristics with the physiological behavior of microtubules. The developed in silico nanoindentation method provides a powerful tool for the exploration of biomechanical properties of other cytoskeletal and multiprotein assemblies. PMID:25389565

  16. Wound healing revised: A novel reepithelialization mechanism revealed by in vitro and in silico models

    PubMed Central

    Safferling, Kai; Sütterlin, Thomas; Westphal, Kathi; Ernst, Claudia; Breuhahn, Kai; James, Merlin; Jäger, Dirk; Halama, Niels

    2013-01-01

    Wound healing is a complex process in which a tissue’s individual cells have to be orchestrated in an efficient and robust way. We integrated multiplex protein analysis, immunohistochemical analysis, and whole-slide imaging into a novel medium-throughput platform for quantitatively capturing proliferation, differentiation, and migration in large numbers of organotypic skin cultures comprising epidermis and dermis. Using fluorescent time-lag staining, we were able to infer source and final destination of keratinocytes in the healing epidermis. This resulted in a novel extending shield reepithelialization mechanism, which we confirmed by computational multicellular modeling and perturbation of tongue extension. This work provides a consistent experimental and theoretical model for epidermal wound closure in 3D, negating the previously proposed concepts of epidermal tongue extension and highlighting the so far underestimated role of the surrounding tissue. Based on our findings, epidermal wound closure is a process in which cell behavior is orchestrated by a higher level of tissue control that 2D monolayer assays are not able to capture. PMID:24385489

  17. In Silico Sequence Analysis Reveals New Characteristics of Fungal NADPH Oxidase Genes

    PubMed Central

    Détry, Nicolas; Choi, Jaeyoung; Kuo, Hsiao-Che; Asiegbu, Fred O.

    2014-01-01

    NADPH oxidases (Noxes), transmembrane proteins found in most eukaryotic species, generate reactive oxygen species and are thereby involved in essential biological processes. However, the fact that genes encoding ferric reductases and ferric-chelate reductases share high sequence similarities and domains with Nox genes represents a challenge for bioinformatic approaches used to identify Nox-encoding genes. Further, most studies on fungal Nox genes have focused mainly on functionality, rather than sequence properties, and consequently clear differentiation among the various Nox isoforms has not been achieved. We conducted an extensive sequence analysis to identify putative Nox genes among 34 eukaryotes, including 28 fungal genomes and one Oomycota genome. Analyses were performed with respect to phylogeny, transmembrane helices, di-histidine distance and glycosylation. Our analyses indicate that the sequence properties of fungal Nox genes are different from those of human and plant Nox genes, thus providing novel insight that will enable more accurate identification and characterization of fungal Nox genes. PMID:25346600

  18. In Silico Prediction of Human Sulfotransferase 1E1 Activity Guided by Pharmacophores from Molecular Dynamics Simulations.

    PubMed

    Rakers, Christin; Schumacher, Fabian; Meinl, Walter; Glatt, Hansruedi; Kleuser, Burkhard; Wolber, Gerhard

    2016-01-01

    Acting during phase II metabolism, sulfotransferases (SULTs) serve detoxification by transforming a broad spectrum of compounds from pharmaceutical, nutritional, or environmental sources into more easily excretable metabolites. However, SULT activity has also been shown to promote formation of reactive metabolites that may have genotoxic effects. SULT subtype 1E1 (SULT1E1) was identified as a key player in estrogen homeostasis, which is involved in many physiological processes and the pathogenesis of breast and endometrial cancer. The development of an in silico prediction model for SULT1E1 ligands would therefore support the development of metabolically inert drugs and help to assess health risks related to hormonal imbalances. Here, we report on a novel approach to develop a model that enables prediction of substrates and inhibitors of SULT1E1. Molecular dynamics simulations were performed to investigate enzyme flexibility and sample protein conformations. Pharmacophores were developed that served as a cornerstone of the model, and machine learning techniques were applied for prediction refinement. The prediction model was used to screen the DrugBank (a database of experimental and approved drugs): 28% of the predicted hits were reported in literature as ligands of SULT1E1. From the remaining hits, a selection of nine molecules was subjected to biochemical assay validation and experimental results were in accordance with the in silico prediction of SULT1E1 inhibitors and substrates, thus affirming our prediction hypotheses. PMID:26542807

  19. In silico Models of Alcohol Dependence and Treatment.

    PubMed

    Kovatchev, Boris; Breton, Marc; Johnson, Bankole

    2012-01-01

    In this paper we view alcohol dependence and the response to treatment as a recurrent bio-behavioral process developing in time and propose formal models of this process combining behavior and biology in silico. The behavioral components of alcohol dependence and treatment are formally described by a stochastic process of human behavior, which serves as an event generator challenging the metabolic system. The biological component is driven by the biochemistry of alcohol intoxication described by deterministic models of ethanol pharmacodynamics and pharmacokinetics to enable simulation of drinking addiction in humans. Derived from the known physiology of ethanol and the literature of both ethanol intoxication and ethanol absorption, the different models are distilled into a minimal model (as simple as the complexity of the data allows) that can represent any specific patient. We use these modeling and simulation techniques to explain responses to placebo and ondansetron treatment observed in clinical studies. Specifically, the response to placebo was explained by a reduction of the probability of environmental reinforcement, while the effect of ondansetron was explained by a gradual decline in the degree of ethanol-induced neuromodulation. Further, we use in silico experiments to study critical transitions in blood alcohol levels after specific average number of drinks per day, and propose the existence of two critical thresholds in the human - one at 5 and another at 11 drinks/day - at which the system shifts from stable to critical and to super critical state indicating a state of alcohol addiction. The advantages of such a model-based investigation are that (1) the process of instigation of alcohol dependence and its treatment can be deconstructed into meaningful steps, which allow for individualized treatment tailoring, and (2) physiology and behavior can be quantified in different (animal or human) studies and then the results can be integrated in silico. PMID

  20. In silico gene expression analysis – an overview

    PubMed Central

    Murray, David; Doran, Peter; MacMathuna, Padraic; Moss, Alan C

    2007-01-01

    Efforts aimed at deciphering the molecular basis of complex disease are underpinned by the availability of high throughput strategies for the identification of biomolecules that drive the disease process. The completion of the human genome-sequencing project, coupled to major technological developments, has afforded investigators myriad opportunities for multidimensional analysis of biological systems. Nowhere has this research explosion been more evident than in the field of transcriptomics. Affordable access and availability to the technology that supports such investigations has led to a significant increase in the amount of data generated. As most biological distinctions are now observed at a genomic level, a large amount of expression information is now openly available via public databases. Furthermore, numerous computational based methods have been developed to harness the power of these data. In this review we provide a brief overview of in silico methodologies for the analysis of differential gene expression such as Serial Analysis of Gene Expression and Digital Differential Display. The performance of these strategies, at both an operational and result/output level is assessed and compared. The key considerations that must be made when completing an in silico expression analysis are also presented as a roadmap to facilitate biologists. Furthermore, to highlight the importance of these in silico methodologies in contemporary biomedical research, examples of current studies using these approaches are discussed. The overriding goal of this review is to present the scientific community with a critical overview of these strategies, so that they can be effectively added to the tool box of biomedical researchers focused on identifying the molecular mechanisms of disease. PMID:17683638

  1. In silico modeling to predict drug-induced phospholipidosis

    SciTech Connect

    Choi, Sydney S.; Kim, Jae S.; Valerio, Luis G. Sadrieh, Nakissa

    2013-06-01

    Drug-induced phospholipidosis (DIPL) is a preclinical finding during pharmaceutical drug development that has implications on the course of drug development and regulatory safety review. A principal characteristic of drugs inducing DIPL is known to be a cationic amphiphilic structure. This provides evidence for a structure-based explanation and opportunity to analyze properties and structures of drugs with the histopathologic findings for DIPL. In previous work from the FDA, in silico quantitative structure–activity relationship (QSAR) modeling using machine learning approaches has shown promise with a large dataset of drugs but included unconfirmed data as well. In this study, we report the construction and validation of a battery of complementary in silico QSAR models using the FDA's updated database on phospholipidosis, new algorithms and predictive technologies, and in particular, we address high performance with a high-confidence dataset. The results of our modeling for DIPL include rigorous external validation tests showing 80–81% concordance. Furthermore, the predictive performance characteristics include models with high sensitivity and specificity, in most cases above ≥ 80% leading to desired high negative and positive predictivity. These models are intended to be utilized for regulatory toxicology applied science needs in screening new drugs for DIPL. - Highlights: • New in silico models for predicting drug-induced phospholipidosis (DIPL) are described. • The training set data in the models is derived from the FDA's phospholipidosis database. • We find excellent predictivity values of the models based on external validation. • The models can support drug screening and regulatory decision-making on DIPL.

  2. Understanding the lid movements of LolA in Escherichia coli using molecular dynamics simulation and in silico point mutation.

    PubMed

    Murahari, Priyadarshini; Anishetty, Sharmila; Pennathur, Gautam

    2013-12-01

    The Lol system in Escherichia coli is involved in localization of lipoproteins and hence is essential for growth of the organism. LolA is a periplasmic chaperone that binds to outer-membrane specific lipoproteins and transports them from inner membrane to outer membrane through LolB. The hydrophobic lipid-binding cavity of LolA consists of α-helices which act as a lid in regulating the transfer of lipoproteins from LolA to LolB. The current study aims to investigate the structural changes observed in LolA during the transition from open to closed conformation in the absence of lipoprotein. Molecular dynamics (MD) simulations were carried out for two LolA crystal structures; LolA(R43L), and in silico mutated MsL43R for a simulation time of 50 ns in water environment. We have performed an in silico point mutation of leucine to arginine in MsL43R to evaluate the importance of arginine to induce structural changes and impact the stability of protein structure. A complete dynamic analysis of open to closed conformation reveals the existence of two distinct levels; closing of lid and closing of entrance of hydrophobic cavity. Our analysis reveals that the structural flexibility of LolA is an important factor for its role as a periplasmic chaperone. PMID:23962984

  3. 2D-DIGE and MALDI TOF/TOF MS analysis reveal that small GTPase signaling pathways may play an important role in cadmium-induced colon cell malignant transformation.

    PubMed

    Lu, Jian; Zhou, Zhongping; Zheng, Jianzhou; Zhang, Zhuyi; Lu, Rongzhu; Liu, Hanqing; Shi, Haifeng; Tu, Zhigang

    2015-10-01

    Cadmium is a toxic heavy metal present in the environment and in industrial materials. Cadmium has demonstrated carcinogenic activity that induces cell transformation, but how this occurs is unclear. We used 2D-DIGE and MALDI TOF/TOF MS combined with bioinformatics and immunoblotting to investigate the molecular mechanism of cadmium transformation. We found that small GTPases were critical for transformation. Additionally, proteins involved in mitochondrial transcription, DNA repair, and translation also had altered expression patterns in cadmium treated cells. Collectively, our results suggest that activation of small GTPases contributes to cadmium-induced transformation of colon cells. PMID:26220685

  4. In silico simulations of experimental protocols for cardiac modeling.

    PubMed

    Carro, Jesus; Rodriguez, Jose Felix; Pueyo, Esther

    2014-01-01

    A mathematical model of the AP involves the sum of different transmembrane ionic currents and the balance of intracellular ionic concentrations. To each ionic current corresponds an equation involving several effects. There are a number of model parameters that must be identified using specific experimental protocols in which the effects are considered as independent. However, when the model complexity grows, the interaction between effects becomes increasingly important. Therefore, model parameters identified considering the different effects as independent might be misleading. In this work, a novel methodology consisting in performing in silico simulations of the experimental protocol and then comparing experimental and simulated outcomes is proposed for parameter model identification and validation. The potential of the methodology is demonstrated by validating voltage-dependent L-type calcium current (ICaL) inactivation in recently proposed human ventricular AP models with different formulations. Our results show large differences between ICaL inactivation as calculated from the model equation and ICaL inactivation from the in silico simulations due to the interaction between effects and/or to the experimental protocol. Our results suggest that, when proposing any new model formulation, consistency between such formulation and the corresponding experimental data that is aimed at being reproduced needs to be first verified considering all involved factors. PMID:25571288

  5. In Silico Analysis of Arabidopsis thaliana Peroxisomal 6-Phosphogluconate Dehydrogenase

    PubMed Central

    Fernández-Fernández, Álvaro D.; Corpas, Francisco J.

    2016-01-01

    NADPH, whose regeneration is critical for reductive biosynthesis and detoxification pathways, is an essential component in cell redox homeostasis. Peroxisomes are subcellular organelles with a complex biochemical machinery involved in signaling and stress processes by molecules such as hydrogen peroxide (H2O2) and nitric oxide (NO). NADPH is required by several peroxisomal enzymes involved in β-oxidation, NO, and glutathione (GSH) generation. Plants have various NADPH-generating dehydrogenases, one of which is 6-phosphogluconate dehydrogenase (6PGDH). Arabidopsis contains three 6PGDH genes that probably are encoded for cytosolic, chloroplastic/mitochondrial, and peroxisomal isozymes, although their specific functions remain largely unknown. This study focuses on the in silico analysis of the biochemical characteristics and gene expression of peroxisomal 6PGDH (p6PGDH) with the aim of understanding its potential function in the peroxisomal NADPH-recycling system. The data show that a group of plant 6PGDHs contains an archetypal type 1 peroxisomal targeting signal (PTS), while in silico gene expression analysis using affymetrix microarray data suggests that Arabidopsis p6PGDH appears to be mainly involved in xenobiotic response, growth, and developmental processes. PMID:27034898

  6. Evolutionary Ensemble for In Silico Prediction of Ames Test Mutagenicity

    NASA Astrophysics Data System (ADS)

    Chen, Huanhuan; Yao, Xin

    Driven by new regulations and animal welfare, the need to develop in silico models has increased recently as alternative approaches to safety assessment of chemicals without animal testing. This paper describes a novel machine learning ensemble approach to building an in silico model for the prediction of the Ames test mutagenicity, one of a battery of the most commonly used experimental in vitro and in vivo genotoxicity tests for safety evaluation of chemicals. Evolutionary random neural ensemble with negative correlation learning (ERNE) [1] was developed based on neural networks and evolutionary algorithms. ERNE combines the method of bootstrap sampling on training data with the method of random subspace feature selection to ensure diversity in creating individuals within an initial ensemble. Furthermore, while evolving individuals within the ensemble, it makes use of the negative correlation learning, enabling individual NNs to be trained as accurate as possible while still manage to maintain them as diverse as possible. Therefore, the resulting individuals in the final ensemble are capable of cooperating collectively to achieve better generalization of prediction. The empirical experiment suggest that ERNE is an effective ensemble approach for predicting the Ames test mutagenicity of chemicals.

  7. Identification of novel drug-resistant EGFR mutant inhibitors by in silico screening using comprehensive assessments of protein structures.

    PubMed

    Sato, Tomohiro; Watanabe, Hisami; Tsuganezawa, Keiko; Yuki, Hitomi; Mikuni, Junko; Yoshikawa, Seiko; Kukimoto-Niino, Mutsuko; Fujimoto, Takako; Terazawa, Yumiko; Wakiyama, Motoaki; Kojima, Hirotatsu; Okabe, Takayoshi; Nagano, Tetsuo; Shirouzu, Mikako; Yokoyama, Shigeyuki; Tanaka, Akiko; Honma, Teruki

    2012-06-15

    EGFR is a target protein for the treatment of non small cell lung cancer (NSCLC). The mutations associated with the activation of EGFR kinase activity, such as L858R and G719S, destabilize the inactive conformation of EGFR and are closely linked with the development of NSCLC. The additional T790M mutation reportedly causes drug resistance against the commercially available EGFR inhibitors, gefitinib and erlotinib. In this study, we searched for novel G719S/T790M EGFR inhibitors by a new in silico screening strategy, using two datasets. The results of in silico screening using protein-ligand docking are affected by the selection of 3D structure of the target protein. As the first strategy, we chose the 3D structures for in silico screening by test dockings using the G719S/T790M crystal structure, its molecular dynamics snapshots, and known inhibitors of the drug-resistant EGFR. In the second strategy, we selected the 3D structures by test dockings using all of the EGFR structures, regardless of the mutations, and all of the known EGFR inhibitors. Using each of the 3D structures selected by the strategies, 1000 compounds were chosen from the 71,588 compounds. Kinase assays identified 15 G719S/T790M EGFR inhibitors, including two compounds with novel scaffolds. Analyses of their structure-activity relationships revealed that interactions with the mutated Met790 residue specifically increase the inhibitory activity against G719S/T790M EGFR. PMID:22607878

  8. Polycyclic aromatic hydrocarbons (PAHs) biodegradation by basidiomycetes fungi, Pseudomonas isolate, and their cocultures: comparative in vivo and in silico approach.

    PubMed

    Arun, A; Raja, P Praveen; Arthi, R; Ananthi, M; Kumar, K Sathish; Eyini, M

    2008-12-01

    The polycyclic aromatic hydrocarbons (PAHs) biodegradation potential of the five basidiomycetes' fungal monocultures and their cocultures was compared with that of a Pseudomonas isolate recovered from oil-spilled soil. As utilization of hydrocarbons by the microorganisms is associated with biosurfactant production, the level of biosurfactant production and its composition by the selected microorganisms was also investigated. The Pseudomonas isolate showed higher ability to degrade three of the five PAHs but the isolate did not produce biosurfactant higher than C. versicolor and P. ostreatus. Among the PAHs, the most effective biodegradation of PAH--pyrene (42%)--was obtained with the fungus C. versicolor. Cocultures involving the fungi and Pseudomonas could not significantly degrade the selected PAHs compounds above that degraded by the most efficient monoculture. A slight increase in pyrene degradation was observed in cocultures of C. versicolor and F. palustris (93.7% pyrene). The crude biosurfactant was biochemically characterized as a multicomponent surfactant consisting of protein and polysaccharides. The PAH biodegradation potential of the basidiomycetes fungi positively correlated with their potential to express ligninolytic enzymes such as lignin peroxidase (Lip), manganese peroxidase (Mnp), and laccase. The present study utilized in silico method such as protein-ligand docking using the FRED in Open Eye software as a tool to assess the level of ligninolytic enzymes and PAHs interactions. The in silico analysis using FRED revealed that of the five PAHs, maximum interaction occurred between pyrene and all the three ligninolytic enzymes. The results of the in silico analysis corroborated with our experimental results showing that pyrene was degraded to the maximum extent by species such as C. versicolor and P. ostreatus. PMID:18975143

  9. In silico analysis and developmental expression of ubiquitin-conjugating enzymes in Schistosoma mansoni.

    PubMed

    Costa, Marcela P; Oliveira, Victor F; Pereira, Roberta V; de Abreu, Fabiano C P; Jannotti-Passos, Liana K; Borges, William C; Guerra-Sá, Renata

    2015-05-01

    Ubiquitin-conjugating enzymes (Ub-E2) perform the second step of ubiquitination and, consequently, are essential for regulating proteolysis and for modulating protein function, interactions and trafficking. Previously, our group demonstrated the crucial role of ubiquitination and the Ub-proteasome pathway during the Schistosoma mansoni life cycle. In the present investigation, we used a homology-based genome-wide bioinformatics approach to identify and molecularly characterise the Ub-E2 enzymes in S. mansoni. The putative functions were further investigated through molecular phylogenetic and expression profile analyses using cercariae, adult worms, eggs and mechanically transformed schistosomula (MTS) cultured in vitro for 3.5 h or 1 or 3 days. We identified, via in silico analysis, 17 Ub-E2 enzymes with conserved structural characteristics: the beta-sheet and the helix-2 form a central core bordered by helix-1 at one side and helix-3 and helix-4 at the other. The observed quantitative differences in the steady-state transcript levels between the cercariae and adult worms may contribute to the differential protein ubiquitination observed during the parasite's life cycle. This study is the first to identify and characterise the E2 ubiquitin conjugation family in S. mansoni and provides fundamental information regarding their molecular phylogenetics and developmental expression during intra-mammalian stages. PMID:25663106

  10. In Silico Inhibition Studies of Jun-Fos-DNA Complex Formation by Curcumin Derivatives

    PubMed Central

    Kumar, Anil; Bora, Utpal

    2012-01-01

    Activator protein-1 (AP1) is a transcription factor that consists of the Jun and Fos family proteins. It regulates gene expression in response to a variety of stimuli and controls cellular processes including proliferation, transformation, inflammation, and innate immune responses. AP1 binds specifically to 12-O-tetradecanoylphorbol-13-acetate (TPA) responsive element 5′-TGAG/CTCA-3′ (AP1 site). It has been found constitutively active in breast, ovarian, cervical, and lung cancers. Numerous studies have shown that inhibition of AP1 could be a promising strategy for cancer therapeutic applications. The present in silico study provides insights into the inhibition of Jun-Fos-DNA complex formation by curcumin derivatives. These derivatives interact with the amino acid residues like Arg155 and Arg158 which play a key role in binding of Jun-Fos complex to DNA (AP1 site). Ala151, Ala275, Leu283, and Ile286 were the residues present at binding site which could contribute to hydrophobic contacts with inhibitor molecules. Curcumin sulphate was predicted to be the most potent inhibitor amongst all the natural curcumin derivatives docked. PMID:25374685

  11. Selection of Mesenchymal-Like Metastatic Cells in Primary Tumors – An in silico Investigation

    PubMed Central

    Narang, Vipin; Wong, Shek Yoon; Leong, Shiang Rong; Harish, Bindu; Abastado, Jean-Pierre; Gouaillard, Alexandre

    2012-01-01

    In order to metastasize, cancer cells must undergo phenotypic transition from an anchorage-dependent form to a motile form via a process referred to as epithelial to mesenchymal transition. It is currently unclear whether metastatic cells emerge late during tumor progression by successive accumulation of mutations, or whether they derive from distinct cell populations already present during the early stages of tumorigenesis. Similarly, the selective pressures that drive metastasis are poorly understood. Selection of cancer cells with increased proliferative capacity and enhanced survival characteristics may explain how some transformations promote a metastatic phenotype. However, it is difficult to explain how cancer cells that disseminate can emerge due to such selective pressure, since these cells usually remain dormant for prolonged periods of time. In the current study, we have used in silico modeling and simulation to investigate the hypothesis that mesenchymal-like cancer cells evolve during the early stages of primary tumor development, and that these cells exhibit survival and proliferative advantages within the tumor microenvironment. In an agent-based tumor microenvironment model, cancer cell agents with distinct sets of attributes governing nutrient consumption, proliferation, apoptosis, random motility, and cell adhesion were allowed to compete for space and nutrients. These simulation data indicated that mesenchymal-like cancer cells displaying high motility and low adhesion proliferate more rapidly and display a survival advantage over epithelial-like cancer cells. Furthermore, the presence of mesenchymal-like cells within the primary tumor influences the macroscopic properties, emergent morphology, and growth rate of tumors. PMID:22566967

  12. Key role of Dkk3 protein in inhibition of cancer cell proliferation: An in silico identification.

    PubMed

    Mohammadpour, Hemn; Pourfathollah, Ali Akbar; Nikougoftar Zarif, Mahin; Khalili, Saeed

    2016-03-21

    Dkk3 is a member of Dkk family proteins, regulating Wnt signaling. Dkk3 plays different roles in human and mouse tumors. Dkk3 predominantly act as a tumor suppressor, however several reports revealed that Dkk3 could accelerate cancer cell proliferation. Herein, we aimed at launching an in silico study to determine Dkk3 structure and its interactions with Kremen and LRP as Wnt signaling receptors as well as EGF receptor. Using various softwares a model was built for Dkk3 molecule. Different protein modeling approaches along with model refinement processes were employed to arrive at the final model. To achieve the final complex of Dkk3 with Kremen, LRP and EGFR molecules protein-protein docking servers were employed. Model assessment softwares indicated the high quality of the finally refined Dkk3 3D structure, indicating the accuracy of modeling and refinement process. Our results revealed that Dkk3 is capable of interacting with Kremen, LRP and EGFR with comparable binding energies. Dkk3 efficiently interacts with LRP, Kremen and EGF receptor and may be a promising protein in cancer therapy by blocking Wnt and EGFR downstream signaling. PMID:26780644

  13. Reading Transformation

    ERIC Educational Resources Information Center

    Reeves, Melinda

    2006-01-01

    The parents of students who attend Decatur High School thought that there was little hope of their kids going on to college. After a year or so in Decatur's reading program, their sons and daughters were both transformed and college bound. In this article, the author describes how Decatur was able to successfully transform their students. Seven…

  14. In silico analysis of deleterious single nucleotide polymorphisms in human BUB1 mitotic checkpoint serine/threonine kinase B gene.

    PubMed

    Akhoundi, Fatemeh; Parvaneh, Nikpour; Modjtaba, Emadi-Baygi

    2016-09-01

    One of the major challenges in the analysis of human genetic variation is to distinguish mutations that are functionally neutral from those that contribute to disease. BubR1 is a key protein mediating spindle-checkpoint activation that plays a role in the inhibition of the anaphase-promoting complex/cyclosome (APC/C), delaying the onset of anaphase and ensuring proper chromosome segregation. Owing to the importance of BUB1B gene in mitotic checkpoint a functional analysis using different in silico approaches was undertaken to explore the possible associations between genetic mutations and phenotypic variation. In this work we found that 3 nsSNPs I82N, P334L and R814H have a functional effect on protein function and stability. A literature search revealed that R814H was already implicated in human diseases. Additionally, 2 SNPs in the 5' UTR region was predicted to exhibit a pattern change in the internal ribosome entry site (IRES), and eight MicroRNA binding sites were found to be highly affected due to 3' UTR SNPs. These in silico predictions will provide useful information in selecting the target SNPs that are likely to have functional impact on the BUB1B gene. PMID:27331020

  15. The current status of time dependent CYP inhibition assay and in silico drug-drug interaction predictions.

    PubMed

    Yan, Zhengyin; Caldwell, Gary W

    2012-01-01

    Various CYP time-dependent inhibition (TDI) assays have been widely implemented in drug discovery and development which has led to great success in positively identifying compounds with mechanism-base inhibition liability. However, drug-drug interaction (DDI) predictions by various in-silico models utilizing kinetic parameters obtained from TDI assays have met with significant challenges including questionable kinetic data, over-simplified in-vitro models and unreliable mathematic algorithms. Although significant efforts have been made to standardize the TDI assay and refine mathematical models, recent evaluation studies have revealed that the kinetic parameters of TDI, the most important in-vitro data required by all DDI prediction models, are significantly impacted by a variety of experimental variables including microsomal protein concentration, metabolic stability, CYP-specific probes, and post-incubation time. This review attempts to provide medicinal chemists a brief overview on the current status of TDI assays, determination of kinetic parameters and in silico DDI predictions with emphasis on the complexity of the TDI kinetics and limitations of current in-vitro models and DDI prediction methodologies. PMID:22571791

  16. Sequence characterization, in silico mapping and cytosine methylation analysis of markers linked to apospory in Paspalum notatum.

    PubMed

    Podio, Maricel; Rodríguez, María P; Felitti, Silvina; Stein, Juliana; Martínez, Eric J; Siena, Lorena A; Quarin, Camilo L; Pessino, Silvina C; Ortiz, Juan Pablo A

    2012-12-01

    In previous studies we reported the identification of several AFLP, RAPD and RFLP molecular markers linked to apospory in Paspalum notatum. The objective of this work was to sequence these markers, obtain their flanking regions by chromosome walking and perform an in silico mapping analysis in rice and maize. The methylation status of two apospory-related sequences was also assessed using methylation-sensitive RFLP experiments. Fourteen molecular markers were analyzed and several protein-coding sequences were identified. Copy number estimates and RFLP linkage analysis showed that the sequence PnMAI3 displayed 2-4 copies per genome and linkage to apospory. Extension of this marker by chromosome walking revealed an additional protein-coding sequence mapping in silico in the apospory-syntenic regions of rice and maize. Approximately 5 kb corresponding to different markers were characterized through the global sequencing procedure. A more refined analysis based on sequence information indicated synteny with segments of chromosomes 2 and 12 of rice and chromosomes 3 and 5 of maize. Two loci associated with apomixis locus were tested in methylation-sensitive RFLP experiments using genomic DNA extracted from leaves. Although both target sequences were methylated no methylation polymorphisms associated with the mode of reproduction were detected. PMID:23271945

  17. In Silico Approach towards Designing Virtual Oligopeptides for HRSV

    PubMed Central

    Jain, Ruchi; Piramanayagam, Shanmughavel

    2014-01-01

    HRSV (human respiratory syncytial virus) is a serious cause of lower respiratory tract illness in infants and young children. Designing inhibitors from the proteins involved in virus replication and infection process provides target for new therapeutic treatments. In the present study, in silico docking was performed using motavizumab as a template to design motavizumab derived oligopeptides for developing novel anti-HRSV agents. Additional simulations were conducted to study the conformational propensities of the oligopeptides and confirmed the hypothesis that the designed oligopeptide is highly flexible and capable of assuming stable confirmation. Our study demonstrated the best specific interaction of GEKKLVEAPKS oligopeptide for glycoprotein strain A among various screened oligopeptides. Encouraged by the results, we expect that the proposed scheme will provide rational choices for antibody reengineering which is useful for systematically identifying the possible ways to improve efficacy of existing antibody drugs. PMID:25525622

  18. In silico design of protein kinase inhibitors: successes and failures.

    PubMed

    Dubinina, Galina G; Chupryna, Oleksandr O; Platonov, Maxim O; Borisko, Petro O; Ostrovska, Galina V; Tolmachov, Andriy O; Shtil, Alexander A

    2007-03-01

    Protein kinases are among the most exploited targets in modern drug discovery due to key roles these enzymes play in human diseases including cancer. The in silico approach, an important part of rational design of protein kinase inhibitors, is founded on vast information about 3D structures of these enzymes. This review summarizes general structural features of the kinase inhibitors and the studies applied toward a large scale chemical database for virtual screening. Analyzed are the ways of validating the modern docking tools and their combinations with different scoring functions. In particular, we discuss the kinase flexibility as a reason for failures of the docking procedure. Finally, evidence is provided for the main patterns of kinase-inhibitor interactions and creation of the hinge-region-directed 2D filters. PMID:17348826

  19. Development of an in Silico Profiler for Mitochondrial Toxicity.

    PubMed

    Nelms, Mark D; Mellor, Claire L; Cronin, Mark T D; Madden, Judith C; Enoch, Steven J

    2015-10-19

    This study outlines the analysis of mitochondrial toxicity for a variety of pharmaceutical drugs extracted from Zhang et al. ((2009) Toxicol. In Vitro, 23, 134-140). These chemicals were grouped into categories based upon structural similarity. Subsequently, mechanistic analysis was undertaken for each category to identify the molecular initiating event driving mitochondrial toxicity. The mechanistic information elucidated during the analysis enabled mechanism-based structural alerts to be developed and combined together to form an in silico profiler. This profiler is envisaged to be used to develop chemical categories based upon similar mechanisms as part of the adverse outcome pathway paradigm. Additionally, the profiler could be utilized in screening large data sets in order to identify chemicals with the potential to induce mitochondrial toxicity. PMID:26375963

  20. In silico substrate dependence increases community productivity but threatens biodiversity

    NASA Astrophysics Data System (ADS)

    Daly, Aisling J.; Baetens, Jan M.; De Baets, Bernard

    2016-04-01

    The critical role that biodiversity plays in ecosystem functioning has motivated many studies of the mechanisms that sustain biodiversity, a notable example being cyclic competition. We extend existing models of communities with cyclic competition by incorporating variable community evenness and resource dependence in demographic processes, two features that have generally been neglected. In this way, we align previous approaches more closely with real-world microbial ecosystems. We demonstrate the existence of a trade-off between increasing biomass production and maintaining biodiversity. This supports experimental observations of a net negative biodiversity effect on biomass productivity, due to competition effects suffered by highly productive species in diverse communities. Our results also support the important role assigned by microbial ecologists to evenness in maintaining ecosystem stability, thus far largely overlooked in in silico approaches.

  1. In silico Exploration of the Conformational Universe of GPCRs.

    PubMed

    Rodríguez-Espigares, Ismael; Kaczor, Agnieszka A; Selent, Jana

    2016-07-01

    The structural plasticity of G protein coupled receptors (GPCRs) leads to a conformational universe going from inactive to active receptor states with several intermediate states. Many of them have not been captured yet and their role for GPCR activation is not well understood. The study of this conformational space and the transition dynamics between different receptor populations is a major challenge in molecular biophysics. The rational design of effector molecules that target such receptor populations allows fine-tuning receptor signalling with higher specificity to produce drugs with safer therapeutic profiles. In this minireview, we outline highly conserved receptor regions which are considered determinant for the establishment of distinct receptor states. We then discuss in-silico approaches such as dimensionality reduction methods and Markov State Models to explore the GPCR conformational universe and exploit the obtained conformations through structure-based drug design. PMID:27492237

  2. Lightweight transformer

    SciTech Connect

    Swallom, D.W.; Enos, G.

    1990-05-01

    The technical effort described in this report relates to the program that was performed to design, fabricate, and test a lightweight transformer for Strategic Defense Initiative Organization (SDIO) mission requirements. The objectives of this program were two-fold: (1) design and fabricate a lightweight transformer using liquid hydrogen as the coolant; and (2) test the completed transformer assembly with a low voltage, dc power source. Although the full power testing with liquid helium was not completed, the program demonstrated the viability of the design approach. The lightweight transformer was designed and fabricated, and low and moderate power testing was completed. The transformer is a liquid hydrogen cooled air core transformer that uses thin copper for its primary and secondary windings. The winding mass was approximately 12 kg, or 0.03 kg/kW. Further refinements of the design to a partial air core transformer could potentially reduce the winding mass to as low as 4 or 5 kg, or 0.0125 kg/kW. No attempt was made on this program to reduce the mass of the related structural components or cryogenic container. 8 refs., 39 figs., 2 tabs.

  3. Understanding complexity in neurodegenerative diseases: in silico reconstruction of emergence

    PubMed Central

    Kolodkin, Alexey; Simeonidis, Evangelos; Balling, Rudi; Westerhoff, Hans V.

    2012-01-01

    Healthy functioning is an emergent property of the network of interacting biomolecules that comprise an organism. It follows that disease (a network shift that causes malfunction) is also an emergent property, emerging from a perturbation of the network. On the one hand, the biomolecular network of every individual is unique and this is evident when similar disease-producing agents cause different individual pathologies. Consequently, a personalized model and approach for every patient may be required for therapies to become effective across mankind. On the other hand, diverse combinations of internal and external perturbation factors may cause a similar shift in network functioning. We offer this as an explanation for the multi-factorial nature of most diseases: they are “systems biology diseases,” or “network diseases.” Here we use neurodegenerative diseases, like Parkinson's disease (PD), as an example to show that due to the inherent complexity of these networks, it is difficult to understand multi-factorial diseases with simply our “naked brain.” When describing interactions between biomolecules through mathematical equations and integrating those equations into a mathematical model, we try to reconstruct the emergent properties of the system in silico. The reconstruction of emergence from interactions between huge numbers of macromolecules is one of the aims of systems biology. Systems biology approaches enable us to break through the limitation of the human brain to perceive the extraordinarily large number of interactions, but this also means that we delegate the understanding of reality to the computer. We no longer recognize all those essences in the system's design crucial for important physiological behavior (the so-called “design principles” of the system). In this paper we review evidence that by using more abstract approaches and by experimenting in silico, one may still be able to discover and understand the design principles that

  4. Improved vanillin production in baker's yeast through in silico design

    PubMed Central

    2010-01-01

    Background Vanillin is one of the most widely used flavouring agents, originally obtained from cured seed pods of the vanilla orchid Vanilla planifolia. Currently vanillin is mostly produced via chemical synthesis. A de novo synthetic pathway for heterologous vanillin production from glucose has recently been implemented in baker's yeast, Saccharamyces cerevisiae. In this study we aimed at engineering this vanillin cell factory towards improved productivity and thereby at developing an attractive alternative to chemical synthesis. Results Expression of a glycosyltransferase from Arabidopsis thaliana in the vanillin producing S. cerevisiae strain served to decrease product toxicity. An in silico metabolic engineering strategy of this vanillin glucoside producing strain was designed using a set of stoichiometric modelling tools applied to the yeast genome-scale metabolic network. Two targets (PDC1 and GDH1) were selected for experimental verification resulting in four engineered strains. Three of the mutants showed up to 1.5 fold higher vanillin β-D-glucoside yield in batch mode, while continuous culture of the Δpdc1 mutant showed a 2-fold productivity improvement. This mutant presented a 5-fold improvement in free vanillin production compared to the previous work on de novo vanillin biosynthesis in baker's yeast. Conclusion Use of constraints corresponding to different physiological states was found to greatly influence the target predictions given minimization of metabolic adjustment (MOMA) as biological objective function. In vivo verification of the targets, selected based on their predicted metabolic adjustment, successfully led to overproducing strains. Overall, we propose and demonstrate a framework for in silico design and target selection for improving microbial cell factories. PMID:21059201

  5. Triple transformation

    NASA Astrophysics Data System (ADS)

    Khan, Farrukh I.; Schinn, Dustin S.

    2013-08-01

    A new business plan that enables policy transformation and resource mobilization at the national and international level, while improving access to resources, will allow the Green Climate Fund to integrate development goals and action on climate change.

  6. Covariant Transform

    NASA Astrophysics Data System (ADS)

    Kisil, Vladimir V.

    2011-03-01

    Dedicated to the memory of Cora Sadosky The paper develops theory of covariant transform, which is inspired by the wavelet construction. It was observed that many interesting types of wavelets (or coherent states) arise from group representations which are not square integrable or vacuum vectors which are not admissible. Covariant transform extends an applicability of the popular wavelets construction to classic examples like the Hardy space H2, Banach spaces, covariant functional calculus and many others.

  7. Transformation of a plasmid-free, genital tract isolate of Chlamydia trachomatis with a plasmid vector carrying a deletion in CDS6 revealed that this gene regulates inclusion phenotype.

    PubMed

    Wang, Yibing; Cutcliffe, Lesley T; Skilton, Rachel J; Persson, Kenneth; Bjartling, Carina; Clarke, Ian N

    2013-03-01

    The development of a plasmid-based genetic transformation protocol for Chlamydia trachomatis provides the basis for the detailed investigation of the function of the chlamydial plasmid and its individual genes or coding sequences (CDS). In this study we constructed a plasmid vector with CDS6 deleted (pCDS6KO) from the original Escherichia coli/C. trachomatis shuttle vector pGFP::SW2. pCDS6KO was transformed into a clinical isolate of C. trachomatis from Sweden that is plasmid-free (C. trachomatis SWFP-). Penicillin-resistant transformants expressing the green fluorescent protein were selected. These transformants did not stain with iodine, indicating that this property is regulated by CDS6 or its gene product. In addition, mature inclusions of C. trachomatis SWFP- transformed by pCDS6KO displayed an identical morphological phenotype to the untransformed plasmid-free recipient host. In this phenotype the morphology of inclusions was altered with the chlamydiae lining the periphery of the inclusion leaving a 'hole' in the centre. These green fluorescent inclusions appear 'doughnut-shaped' with an empty centre when examined under blue light, giving rise to a characteristic 'black hole' phenotype. Our study demonstrates the power of the new genetic system for investigating chlamydial gene function using gene deletion technology. PMID:23620154

  8. Transformation of a plasmid-free, genital tract isolate of Chlamydia trachomatis with a plasmid vector carrying a deletion in CDS6 revealed that this gene regulates inclusion phenotype

    PubMed Central

    Wang, Yibing; Cutcliffe, Lesley T; Skilton, Rachel J; Persson, Kenneth; Bjartling, Carina; Clarke, Ian N

    2013-01-01

    The development of a plasmid-based genetic transformation protocol for Chlamydia trachomatis provides the basis for the detailed investigation of the function of the chlamydial plasmid and its individual genes or coding sequences (CDS). In this study we constructed a plasmid vector with CDS6 deleted (pCDS6KO) from the original Escherichia coli/C. trachomatis shuttle vector pGFP::SW2. pCDS6KO was transformed into a clinical isolate of C. trachomatis from Sweden that is plasmid-free (C. trachomatis SWFP–). Penicillin-resistant transformants expressing the green fluorescent protein were selected. These transformants did not stain with iodine, indicating that this property is regulated by CDS6 or its gene product. In addition, mature inclusions of C. trachomatis SWFP– transformed by pCDS6KO displayed an identical morphological phenotype to the untransformed plasmid-free recipient host. In this phenotype the morphology of inclusions was altered with the chlamydiae lining the periphery of the inclusion leaving a ‘hole’ in the centre. These green fluorescent inclusions appear ‘doughnut-shaped’ with an empty centre when examined under blue light, giving rise to a characteristic ‘black hole’ phenotype. Our study demonstrates the power of the new genetic system for investigating chlamydial gene function using gene deletion technology. PMID:23620154

  9. DockScreen: A database of in silico biomolecular interactions to support computational toxicology

    EPA Science Inventory

    We have developed DockScreen, a database of in silico biomolecular interactions designed to enable rational molecular toxicological insight within a computational toxicology framework. This database is composed of chemical/target (receptor and enzyme) binding scores calculated by...

  10. Ensuring confidence in predictions: A scheme to assess the scientific validity of in silico models.

    PubMed

    Hewitt, Mark; Ellison, Claire M; Cronin, Mark T D; Pastor, Manuel; Steger-Hartmann, Thomas; Munoz-Muriendas, Jordi; Pognan, Francois; Madden, Judith C

    2015-06-23

    The use of in silico tools within the drug development process to predict a wide range of properties including absorption, distribution, metabolism, elimination and toxicity has become increasingly important due to changes in legislation and both ethical and economic drivers to reduce animal testing. Whilst in silico tools have been used for decades there remains reluctance to accept predictions based on these methods particularly in regulatory settings. This apprehension arises in part due to lack of confidence in the reliability, robustness and applicability of the models. To address this issue we propose a scheme for the verification of in silico models that enables end users and modellers to assess the scientific validity of models in accordance with the principles of good computer modelling practice. We report here the implementation of the scheme within the Innovative Medicines Initiative project "eTOX" (electronic toxicity) and its application to the in silico models developed within the frame of this project. PMID:25794480

  11. Stochastic Drift in Mitochondrial DNA Point Mutations: A Novel Perspective Ex Silico

    PubMed Central

    Poovathingal, Suresh Kumar; Gruber, Jan; Halliwell, Barry; Gunawan, Rudiyanto

    2009-01-01

    The mitochondrial free radical theory of aging (mFRTA) implicates Reactive Oxygen Species (ROS)-induced mutations of mitochondrial DNA (mtDNA) as a major cause of aging. However, fifty years after its inception, several of its premises are intensely debated. Much of this uncertainty is due to the large range of values in the reported experimental data, for example on oxidative damage and mutational burden in mtDNA. This is in part due to limitations with available measurement technologies. Here we show that sample preparations in some assays necessitating high dilution of DNA (single molecule level) may introduce significant statistical variability. Adding to this complexity is the intrinsically stochastic nature of cellular processes, which manifests in cells from the same tissue harboring varying mutation load. In conjunction, these random elements make the determination of the underlying mutation dynamics extremely challenging. Our in silico stochastic study reveals the effect of coupling the experimental variability and the intrinsic stochasticity of aging process in some of the reported experimental data. We also show that the stochastic nature of a de novo point mutation generated during embryonic development is a major contributor of different mutation burdens in the individuals of mouse population. Analysis of simulation results leads to several new insights on the relevance of mutation stochasticity in the context of dividing tissues and the plausibility of ROS ”vicious cycle” hypothesis. PMID:19936024

  12. An in silico expert system for the identification of eye irritants.

    PubMed

    Verma, R P; Matthews, E J

    2015-01-01

    This report describes development of an in silico, expert rule-based method for the classification of chemicals into irritants or non-irritants to eye, as defined by the Draize test. This method was developed to screen data-poor cosmetic ingredient chemicals for eye irritancy potential, which is based upon exclusion rules of five physicochemical properties - molecular weight (MW), hydrophobicity (log P), number of hydrogen bond donors (HBD), number of hydrogen bond acceptors (HBA) and polarizability (Pol). These rules were developed using the ADMET Predictor software and a dataset of 917 eye irritant chemicals. The dataset was divided into 826 (90%) chemicals used for training set and 91 (10%) chemicals used for external validation set (every 10th chemical sorted by molecular weight). The sensitivity of these rules for the training and validation sets was 72.3% and 71.4%, respectively. These rules were also validated for their specificity using an external validation set of 2011 non-irritant chemicals to the eye. The specificity for this validation set was revealed as 77.3%. This method facilitates rapid screening and prioritization of data poor chemicals that are unlikely to be tested for eye irritancy in the Draize test. PMID:25967253

  13. In silico identification of coffee genome expressed sequences potentially associated with resistance to diseases

    PubMed Central

    2010-01-01

    Sequences potentially associated with coffee resistance to diseases were identified by in silico analyses using the database of the Brazilian Coffee Genome Project (BCGP). Keywords corresponding to plant resistance mechanisms to pathogens identified in the literature were used as baits for data mining. Expressed sequence tags (ESTs) related to each of these keywords were identified with tools available in the BCGP bioinformatics platform. A total of 11,300 ESTs were mined. These ESTs were clustered and formed 979 EST-contigs with similarities to chitinases, kinases, cytochrome P450 and nucleotide binding site-leucine rich repeat (NBS-LRR) proteins, as well as with proteins related to disease resistance, pathogenesis, hypersensitivity response (HR) and plant defense responses to diseases. The 140 EST-contigs identified through the keyword NBS-LRR were classified according to function. This classification allowed association of the predicted products of EST-contigs with biological processes, including host defense and apoptosis, and with molecular functions such as nucleotide binding and signal transducer activity. Fisher's exact test was used to examine the significance of differences in contig expression between libraries representing the responses to biotic stress challenges and other libraries from the BCGP. This analysis revealed seven contigs highly similar to catalase, chitinase, protein with a BURP domain and unknown proteins. The involvement of these coffee proteins in plant responses to disease is discussed. PMID:21637594

  14. Isolation and in silico evaluation of antidiabetic molecules of Cynodon dactylon (L.).

    PubMed

    Annapurna, Hasthi V; Apoorva, Babu; Ravichandran, Natesan; Arun, Kallur Purushothaman; Brindha, Pemaiah; Swaminathan, Sethuraman; Vijayalakshmi, Mahadevan; Nagarajan, Arumugam

    2013-02-01

    Cynodon dactylon is a potential source of metabolites such as flavanoids, alkaloids, glycosides and β-sitosterol and has been traditionally employed to treat urinary tract and other microbial infections and dysentery. The present work attempts to evaluate the activity of C. dactylon extracts for glycemic control. Aqueous extracts of C. dactylon analyzed by HPLC-ESI MS have identified the presence of apigenin, luteolin, 6-C-pentosyl-8-C-hexosyl apigenin and 6-C-hexosyl-8-C-pentosyl luteolin. Evaluation of hypoglycemic activity through an extensive in silico docking approach with PPARγ (Peroxisome Proliferator-Activated Receptor), GLUT-4 (glucose transporter-4) and SGLT2 (sodium glucose co-transporter-2) revealed that luteolin, apigenin, 6-C-pentosyl-8-C-hexosyl apigenin, 6-C-hexosyl-8-C-pentosyl luteolin interact with SGLT2. Interactions of these molecules with Gln 295 and Asp 294 residues of SGLT2 have been shown to compare well with that of the phase III drug, dapagliflozin. These residues have been proven to be responsible for sugar sensing and transport. This work establishes C. dactylon extract as a potential SGLT2 inhibitor for diabetic neuropathy thus enabling a possibility of this plant extract as a new alternative to existing diabetic approaches. PMID:23261878

  15. Permethrin is a potential thyroid-disrupting chemical: In vivo and in silico envidence.

    PubMed

    Tu, Wenqing; Xu, Chao; Jin, Yuanxiang; Lu, Bin; Lin, Chunmian; Wu, Yongming; Liu, Weiping

    2016-06-01

    Permethrin (PM), one of the most heavily used synthetic pyrethroids, has the potential to interfere with thyroid hormones in mammals, however, the effect is poorly recognized in aquatic organisms. Herein, embryonic zebrafish were exposed to PM (0, 1, 3 and 10μg/L) until 72h post-fertilization. We demonstrated that PM readily accumulated in larvae with a preference for cis-PM, inhibited development and increased thyroxine and 3,5,3'-triiodothyronine levels accompanying increase in the transcription of most target genes, i.e., thyroid-stimulating hormone β, deiodinases, thyroid receptors, involved in the hypothalamic-pituitary-thyroid axis. Further Western blot analysis indicated that transthyretin (TTR) protein was significantly increased. Molecular docking analysis and molecular dynamics simulations revealed that PM fits into three hydrophobic binding pocket of TTR, one of the molecular targets of thyroid hormone disrupting chemicals (THDCs), and forms strong van der Waals interactions with six resides of TTR, including Leu8, Leu 101, Leu125, Thr214, Leu218 and Val229, thus altering TTR activity. Both in vivo and in silico studies clearly disclosed that PM potentially disrupts the thyroid endocrine system in fish. This study provides a rapid and cost-effective approach for identifying THDCs and the underlying mechanisms. PMID:26994367

  16. Cloning, Sequencing, and In Silico Analysis of β-Propeller Phytase Bacillus licheniformis Strain PB-13

    PubMed Central

    Sangwan, Punesh; Verma, A. K.; Agrawal, Sanjeev

    2014-01-01

    β-Propeller phytases (BPPhy) are widely distributed in nature and play a major role in phytate-phosphorus cycling. In the present study, a BPPhy gene from Bacillus licheniformis strain was expressed in E. coli with a phytase activity of 1.15 U/mL and specific activity of 0.92 U/mg proteins. The expressed enzyme represented a full length ORF “PhyPB13” of 381 amino acid residues and differs by 3 residues from the closest similar existing BPPhy sequences. The PhyPB13 sequence was characterized in silico using various bioinformatic tools to better understand structural, functional, and evolutionary aspects of BPPhy class by multiple sequence alignment and homology search, phylogenetic tree construction, variation in biochemical features, and distribution of motifs and superfamilies. In all sequences, conserved sites were observed toward their N-terminus and C-terminus. Cysteine was not present in the sequence. Overall, three major clusters were observed in phylogenetic tree with variation in biophysical characteristics. A total of 10 motifs were reported with motif “1” observed in all 44 protein sequences and might be used for diversity and expression analysis of BPPhy enzymes. This study revealed important sequence features of BPPhy and pave a way for determining catalytic mechanism and selection of phytase with desirable characteristics. PMID:24864215

  17. In Silico Analysis of Microarray-Based Gene Expression Profiles Predicts Tumor Cell Response to Withanolides

    PubMed Central

    Efferth, Thomas; Greten, Henry Johannes

    2012-01-01

    Withania somnifera (L.) Dunal (Indian ginseng, winter cherry, Solanaceae) is widely used in traditional medicine. Roots are either chewed or used to prepare beverages (aqueous decocts). The major secondary metabolites of Withania somnifera are the withanolides, which are C-28-steroidal lactone triterpenoids. Withania somnifera extracts exert chemopreventive and anticancer activities in vitro and in vivo. The aims of the present in silico study were, firstly, to investigate whether tumor cells develop cross-resistance between standard anticancer drugs and withanolides and, secondly, to elucidate the molecular determinants of sensitivity and resistance of tumor cells towards withanolides. Using IC50 concentrations of eight different withanolides (withaferin A, withaferin A diacetate, 3-azerininylwithaferin A, withafastuosin D diacetate, 4-B-hydroxy-withanolide E, isowithanololide E, withafastuosin E, and withaperuvin) and 19 established anticancer drugs, we analyzed the cross-resistance profile of 60 tumor cell lines. The cell lines revealed cross-resistance between the eight withanolides. Consistent cross-resistance between withanolides and nitrosoureas (carmustin, lomustin, and semimustin) was also observed. Then, we performed transcriptomic microarray-based COMPARE and hierarchical cluster analyses of mRNA expression to identify mRNA expression profiles predicting sensitivity or resistance towards withanolides. Genes from diverse functional groups were significantly associated with response of tumor cells to withaferin A diacetate, e.g. genes functioning in DNA damage and repair, stress response, cell growth regulation, extracellular matrix components, cell adhesion and cell migration, constituents of the ribosome, cytoskeletal organization and regulation, signal transduction, transcription factors, and others.

  18. Quercetin Influences Quorum Sensing in Food Borne Bacteria: In-Vitro and In-Silico Evidence

    PubMed Central

    Gopu, Venkadesaperumal; Meena, Chetan Kumar; Shetty, Prathapkumar Halady

    2015-01-01

    Quorum sensing (QS) plays a vital role in regulating the virulence factor of many food borne pathogens, which causes severe public health risk. Therefore, interrupting the QS signaling pathway may be an attractive strategy to combat microbial infections. In the current study QS inhibitory activity of quercetin and its anti-biofilm property was assessed against food-borne pathogens using a bio-sensor strain. In addition in-silico techniques like molecular docking and molecular dynamics simulation studies were applied to screen the quercetin’s potentiality as QS inhibitor. Quercetin (80μg/ml) showed the significant reduction in QS-dependent phenotypes like violacein production, biofilm formation, exopolysaccharide (EPS) production, motility and alginate production in a concentration-dependent manner. Synergistic activity of conventional antibiotics with quercetin enhanced the susceptibility of all tested pathogens. Furthermore, Molecular docking analysis revealed that quercetin binds more rigidly with LasR receptor protein than the signaling compound with docking score of -9.17Kcal/mol. Molecular dynamics simulation predicted that QS inhibitory activity of quercetin occurs through the conformational changes between the receptor and quercetin complex. Above findings suggest that quercetin can act as a competitive inhibitor for signaling compound towards LasR receptor pathway and can serve as a novel QS-based antibacterial/anti-biofilm drug to manage food-borne pathogens. PMID:26248208

  19. In silico identification of coffee genome expressed sequences potentially associated with resistance to diseases.

    PubMed

    Alvarenga, Samuel Mazzinghy; Caixeta, Eveline Teixeira; Hufnagel, Bárbara; Thiebaut, Flávia; Maciel-Zambolim, Eunize; Zambolim, Laércio; Sakiyama, Ney Sussumu

    2010-10-01

    Sequences potentially associated with coffee resistance to diseases were identified by in silico analyses using the database of the Brazilian Coffee Genome Project (BCGP). Keywords corresponding to plant resistance mechanisms to pathogens identified in the literature were used as baits for data mining. Expressed sequence tags (ESTs) related to each of these keywords were identified with tools available in the BCGP bioinformatics platform. A total of 11,300 ESTs were mined. These ESTs were clustered and formed 979 EST-contigs with similarities to chitinases, kinases, cytochrome P450 and nucleotide binding site-leucine rich repeat (NBS-LRR) proteins, as well as with proteins related to disease resistance, pathogenesis, hypersensitivity response (HR) and plant defense responses to diseases. The 140 EST-contigs identified through the keyword NBS-LRR were classified according to function. This classification allowed association of the predicted products of EST-contigs with biological processes, including host defense and apoptosis, and with molecular functions such as nucleotide binding and signal transducer activity. Fisher's exact test was used to examine the significance of differences in contig expression between libraries representing the responses to biotic stress challenges and other libraries from the BCGP. This analysis revealed seven contigs highly similar to catalase, chitinase, protein with a BURP domain and unknown proteins. The involvement of these coffee proteins in plant responses to disease is discussed. PMID:21637594

  20. In Silico Investigation of Potential Src Kinase Ligands from Traditional Chinese Medicine

    PubMed Central

    Tou, Weng Ieong; Chen, Calvin Yu-Chian

    2012-01-01

    Src kinase is an attractive target for drug development based on its established relationship with cancer and possible link to hypertension. The suitability of traditional Chinese medicine (TCM) compounds as potential drug ligands for further biological evaluation was investigated using structure-based, ligand-based, and molecular dynamics (MD) analysis. Isopraeroside IV, 9alpha-hydroxyfraxinellone-9-O-beta-D-glucoside (9HFG) and aurantiamide were the top three TCM candidates identified from docking. Hydrogen bonds and hydrophobic interactions were the primary forces governing docking stability. Their stability with Src kinase under a dynamic state was further validated through MD and torsion angle analysis. Complexes formed by TCM candidates have lower total energy estimates than the control Sacaratinib. Four quantitative-structural activity relationship (QSAR) in silico verifications consistently suggested that the TCM candidates have bioactive properties. Docking conformations of 9HFG and aurantiamide in the Src kinase ATP binding site suggest potential inhibitor-like characteristics, including competitive binding at the ATP binding site (Lys295) and stabilization of the catalytic cleft integrity. The TCM candidates have significantly lower ligand internal energies and are estimated to form more stable complexes with Src kinase than Saracatinib. Structure-based and ligand-based analysis support the drug-like potential of 9HFG and aurantiamide and binding mechanisms reveal the tendency of these two candidates to compete for the ATP binding site. PMID:22470466

  1. In-silico Investigation of Antitrypanosomal Phytochemicals from Nigerian Medicinal Plants

    PubMed Central

    Setzer, William N.; Ogungbe, Ifedayo V.

    2012-01-01

    Background Human African trypanosomiasis (HAT), a parasitic protozoal disease, is caused primarily by two subspecies of Trypanosoma brucei. HAT is a re-emerging disease and currently threatens millions of people in sub-Saharan Africa. Many affected people live in remote areas with limited access to health services and, therefore, rely on traditional herbal medicines for treatment. Methods A molecular docking study has been carried out on phytochemical agents that have been previously isolated and characterized from Nigerian medicinal plants, either known to be used ethnopharmacologically to treat parasitic infections or known to have in-vitro antitrypanosomal activity. A total of 386 compounds from 19 species of medicinal plants were investigated using in-silico molecular docking with validated Trypanosoma brucei protein targets that were available from the Protein Data Bank (PDB): Adenosine kinase (TbAK), pteridine reductase 1 (TbPTR1), dihydrofolate reductase (TbDHFR), trypanothione reductase (TbTR), cathepsin B (TbCatB), heat shock protein 90 (TbHSP90), sterol 14α-demethylase (TbCYP51), nucleoside hydrolase (TbNH), triose phosphate isomerase (TbTIM), nucleoside 2-deoxyribosyltransferase (TbNDRT), UDP-galactose 4′ epimerase (TbUDPGE), and ornithine decarboxylase (TbODC). Results This study revealed that triterpenoid and steroid ligands were largely selective for sterol 14α-demethylase; anthraquinones, xanthones, and berberine alkaloids docked strongly to pteridine reductase 1 (TbPTR1); chromenes, pyrazole and pyridine alkaloids preferred docking to triose phosphate isomerase (TbTIM); and numerous indole alkaloids showed notable docking energies with UDP-galactose 4′ epimerase (TbUDPGE). Polyphenolic compounds such as flavonoid gallates or flavonoid glycosides tended to be promiscuous docking agents, giving strong docking energies with most proteins. Conclusions This in-silico molecular docking study has identified potential biomolecular targets of

  2. An RNAi in silico approach to find an optimal shRNA cocktail against HIV-1

    PubMed Central

    2010-01-01

    Background HIV-1 can be inhibited by RNA interference in vitro through the expression of short hairpin RNAs (shRNAs) that target conserved genome sequences. In silico shRNA design for HIV has lacked a detailed study of virus variability constituting a possible breaking point in a clinical setting. We designed shRNAs against HIV-1 considering the variability observed in naïve and drug-resistant isolates available at public databases. Methods A Bioperl-based algorithm was developed to automatically scan multiple sequence alignments of HIV, while evaluating the possibility of identifying dominant and subdominant viral variants that could be used as efficient silencing molecules. Student t-test and Bonferroni Dunn correction test were used to assess statistical significance of our findings. Results Our in silico approach identified the most common viral variants within highly conserved genome regions, with a calculated free energy of ≥ -6.6 kcal/mol. This is crucial for strand loading to RISC complex and for a predicted silencing efficiency score, which could be used in combination for achieving over 90% silencing. Resistant and naïve isolate variability revealed that the most frequent shRNA per region targets a maximum of 85% of viral sequences. Adding more divergent sequences maintained this percentage. Specific sequence features that have been found to be related with higher silencing efficiency were hardly accomplished in conserved regions, even when lower entropy values correlated with better scores. We identified a conserved region among most HIV-1 genomes, which meets as many sequence features for efficient silencing. Conclusions HIV-1 variability is an obstacle to achieving absolute silencing using shRNAs designed against a consensus sequence, mainly because there are many functional viral variants. Our shRNA cocktail could be truly effective at silencing dominant and subdominant naïve viral variants. Additionally, resistant isolates might be targeted

  3. SHARP transformation

    NASA Astrophysics Data System (ADS)

    Wyatt, Stephan

    2004-08-01

    The U.S. Navy"s SHAred Reconnaissance Pod (SHARP) employs the Recon/Optical, Inc. (ROI) CA-279 dual spectral band (visible/IR) digital cameras operating from an F-18E/F aircraft to perform low-to-high altitude reconnaissance missions. SHARP has proven itself combat worthy, with a rapid transition from development to operational deployment culminating in a highly reliable and effective reconnaissance capability for joint forces operating in Operation Iraqi Freedom (OIF). The U.S. Navy"s intelligence, surveillance and reconnaissance (ISR) roadmap transforms the SHARP system from being solely an independent reconnaissance sensor to a node in the growing Joint ISR network. ROI and the U.S. Navy have combined their resources to ensure the system"s transformation continues to follow the ISR road map. Pre-planned product improvements (P3I) for the CA-270 camera systems will lead the way in that transformation.

  4. Translating and Transforming Care

    PubMed Central

    Gillespie, Alex; Moore, Helen

    2015-01-01

    This article examines how the Disability Living Allowance claim form, used in the United Kingdom to allocate £13 billion of disability benefits, translates and transforms disability and care. Twenty-two people with acquired brain injury and their main informal caregivers (n = 44) were video-recorded filling in the disability claim form. Participants disagreed on 26% of the questions, revealing two types of problems. Translation problems arose as participants struggled to provide categorical responses to ambiguous questions and were unable to report contextual variability in care needs or divergences of perception. Transformation problems arose as participants resisted the way in which the form positioned them, forcing them to conceptualize their relationship in terms of dependency and burden. The disability claim form co-opts claimants to translate care and disability into bureaucratically predefined categories, and it transforms the care relationship that it purports to document. PMID:25792487

  5. Alterations of auxin perception in rolB-transformed tobacco protoplasts. Time course of rolB mRNA expression and increase in auxin sensitivity reveal multiple control by auxin.

    PubMed Central

    Maurel, C; Leblanc, N; Barbier-Brygoo, H; Perrot-Rechenmann, C; Bouvier-Durand, M; Guern, J

    1994-01-01

    Expression and physiological effects of the root-inducing rolB gene of Agrobacterium rhizogenes T-DNA were studied simultaneously in tobacco (Nicotiana tabacum) mesophyll protoplasts. The kinetic study of the expression of rolB mRNA following exogenous auxin application showed that auxin transiently stimulated rolB expression, with mRNA levels starting to accumulate 6 to 9 h after auxin was supplied and increasing 300-fold after 12 to 18 h. The parallel study of the auxin sensitivity of rolB-transformed protoplasts, as assayed by their electrical response to the hormone, showed that the auxin treatment generated an increase in sensitivity by a factor of up to 100,000, whereas in untransformed protoplasts the same auxin treatment induced an increase in auxin sensitivity that never exceeded 30- to 50-fold. This reflects a strong cooperative effect of auxin and rolB in transformed protoplasts. Surprisingly, the maximal increase in sensitivity was observed several hours before the maximal accumulation of rolB mRNA, suggesting that the dramatic control of auxin sensitivity by auxin in rolB-transformed protoplasts requires only low levels of rolB expression. Antibodies directed against ZmER-abp1, the major auxin-binding protein from maize, differentially altered the auxin sensitivity of the electrical response of rolB-transformed and normal protoplasts. This suggests that alterations of the auxin reception-transduction pathway at the plasma membrane of rolB-transformed protoplasts may account for their increased auxin sensitivity. PMID:7972494

  6. In silico analysis of the regulatory region of the Yellowtail Kingfish and Zebrafish Kiss and Kiss receptor genes.

    PubMed

    Nocillado, J N; Mechaly, A S; Elizur, A

    2013-02-01

    We have cloned and analysed the partial putative promoter sequences of the Yellowtail Kingfish (Seriola lalandi) Kiss2 and Kiss2r genes (380 and 420 bp, respectively). We obtained in silico 1.5 kb of the zebrafish (Danio rerio) Kiss1, Kiss2, Kiss1r and zfKiss2r sequences upstream of the putative transcriptional initiation site. Bioinformatic analysis revealed promoter regulatory elements including AP-1, Sp1, GR, ER, PR, AR, GATA-1, TTF-1, YY1 and C/EBP. These regulatory elements may mediate novel roles of the Kiss genes and their receptors in addition to their established role in reproductive function. PMID:22527613

  7. Progress in predicting human ADME parameters in silico.

    PubMed

    Ekins, S; Waller, C L; Swaan, P W; Cruciani, G; Wrighton, S A; Wikel, J H

    2000-01-01

    evaluation of higher throughput data to determine if computational (in silico) models can be constructed and validated from it. Such models would allow an exponential increase in the number of compounds screened virtually for ADME parameters. A number of researchers have started to utilize in silico, in vitro and in vivo approaches in parallel to address intestinal permeability and cytochrome P-450-mediated DDI. This review will assess how computational approaches for ADME parameters have evolved and how they are likely to progress. PMID:11274894

  8. AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening

    PubMed Central

    Pencheva, Tania; Lagorce, David; Pajeva, Ilza; Villoutreix, Bruno O; Miteva, Maria A

    2008-01-01

    Background Virtual or in silico ligand screening combined with other computational methods is one of the most promising methods to search for new lead compounds, thereby greatly assisting the drug discovery process. Despite considerable progresses made in virtual screening methodologies, available computer programs do not easily address problems such as: structural optimization of compounds in a screening library, receptor flexibility/induced-fit, and accurate prediction of protein-ligand interactions. It has been shown that structural optimization of chemical compounds and that post-docking optimization in multi-step structure-based virtual screening approaches help to further improve the overall efficiency of the methods. To address some of these points, we developed the program AMMOS for refining both, the 3D structures of the small molecules present in chemical libraries and the predicted receptor-ligand complexes through allowing partial to full atom flexibility through molecular mechanics optimization. Results The program AMMOS carries out an automatic procedure that allows for the structural refinement of compound collections and energy minimization of protein-ligand complexes using the open source program AMMP. The performance of our package was evaluated by comparing the structures of small chemical entities minimized by AMMOS with those minimized with the Tripos and MMFF94s force fields. Next, AMMOS was used for full flexible minimization of protein-ligands complexes obtained from a mutli-step virtual screening. Enrichment studies of the selected pre-docked complexes containing 60% of the initially added inhibitors were carried out with or without final AMMOS minimization on two protein targets having different binding pocket properties. AMMOS was able to improve the enrichment after the pre-docking stage with 40 to 60% of the initially added active compounds found in the top 3% to 5% of the entire compound collection. Conclusion The open source AMMOS

  9. Time-Dependent Inhibition of CYP2C19 by Isoquinoline Alkaloids: In Vitro and In Silico Analysis.

    PubMed

    Salminen, Kaisa A; Rahnasto-Rilla, Minna; Väänänen, Raija; Imming, Peter; Meyer, Achim; Horling, Aline; Poso, Antti; Laitinen, Tuomo; Raunio, Hannu; Lahtela-Kakkonen, Maija

    2015-12-01

    The cytochrome P450 2C19 (CYP2C19) enzyme plays an important role in the metabolism of many commonly used drugs. Relatively little is known about CYP2C19 inhibitors, including compounds of natural origin, which could inhibit CYP2C19, potentially causing clinically relevant metabolism-based drug interactions. We evaluated a series (N = 49) of structurally related plant isoquinoline alkaloids for their abilities to interact with CYP2C19 enzyme using in vitro and in silico methods. We examined several common active alkaloids found in herbal products such as apomorphine, berberine, noscapine, and papaverine, as well as the previously identified mechanism-based inactivators bulbocapnine, canadine, and protopine. The IC50 values of the alkaloids ranged from 0.11 to 210 µM, and 42 of the alkaloids were confirmed to be time-dependent inhibitors of CYP2C19. Molecular docking and three-dimensional quantitative structure-activity relationship analysis revealed key interactions of the potent inhibitors with the enzyme active site. We constructed a comparative molecular field analysis model that was able to predict the inhibitory potency of a series of independent test molecules. This study revealed that many of these isoquinoline alkaloids do have the potential to cause clinically relevant drug interactions. These results highlight the need for studying more profoundly the potential interactions between drugs and herbal products. When further refined, in silico methods can be useful in the high-throughput prediction of P450 inhibitory potential of pharmaceutical compounds. PMID:26400396

  10. A report of rifampin-resistant leprosy from northern and eastern India: identification and in silico analysis of molecular interactions.

    PubMed

    Vedithi, Sundeep Chaitanya; Lavania, Mallika; Kumar, Manoj; Kaur, Punit; Turankar, Ravindra P; Singh, Itu; Nigam, Astha; Sengupta, Utpal

    2015-04-01

    Presence of point mutations within the drug resistance determining regions of Mycobacterium leprae (M. leprae) genome confers molecular basis of drug resistance to dapsone, rifampin and ofloxacin in leprosy. This study is focused on the identification of mutations within the rpoB gene region of M. leprae that are specific for rifampin interaction, and further in silico analysis was carried out to determine the variations in the interactions. DNA and RNA were isolated from slit skin scrapings of 60 relapsed leprosy patients. PCR targeting rpoB gene region and amplicon sequencing was performed to determine point mutations. mRNA expression levels of rpoB and high-resolution melt analysis of mutants were performed using Rotor Gene Q Realtime PCR. Molecular docking was performed using LigandFit Software. Ten cases having point mutations within the rpoB gene region were identified and were clinically confirmed to be resistant to rifampin. A new mutation at codon position Gln442His has been identified. There is a 9.44-fold upregulation in the mRNA expression of rpoB gene in mutant/resistant samples when compared with the wild/sensitive samples. In silico docking analysis of rifampin with wild-type and Gln442His mutant RpoB proteins revealed a variation in the hydrogen-bonding pattern leading to a difference in the total interaction energy and conformational change at position Asp441. These preliminary downstream functional observations revealed that the presence of point mutations within the rifampin resistance determining regions of rpoB gene plays a vital role in conferring genetic and molecular basis of resistance to rifampin in leprosy. PMID:25201810

  11. Toxicity study of dibutyl phthalate of Rubia cordifolia fruits: in vivo and in silico analysis.

    PubMed

    Anantharaman, Amrita; Priya, Rajendra Rao; Hemachandran, Hridya; Akella, Sivaramakrishna; Rajasekaran, Chandrasekaran; Ganesh, Jai; Fulzele, Devanand P; Siva, Ramamoorthy

    2016-09-01

    Natural toxins from plant sources with wide ranges of biological activities reflect the upswing of drug design in the pharmaceutical industry. Rubia cordifolia L. is one of the most important red dye yielding plants. Most of the former researches have focused on the bioactive compounds from the roots of R. cordifolia, while no attention was paid towards the fruits. For the first time, here we report the presence of dibutyl phthalate in the fruits of R. cordifolia. Structural characterization was carried out using Ultraviolet-Visible spectrophotometer (UV-Vis), Fourier transform infrared (FTIR), gas chromatography-mass spectrophotometer (GC-MS), Nuclear magnetic resonance (NMR). Acute toxicity of the crude ethanolic extracts of the R. cordifolia fruits was examined in Swiss albino mice. No mortality was observed in all treated mice with 100, 500, 1000 mg/kg body weight of crude extract of R. cordifolia fruit and it indicates that the LD50 value is higher than 1000 mg/kg body weight. This study exhibited a significant change in the body weight. Alanine transaminase (ALT), total protein, triglycerides, glucose, and also the histopathological analysis of liver for all treated mice showed difference from the control group. The dibutyl phthalate was further evaluated for the toxicity study through in silico analysis. Together, the results highlighted that the toxic potential of R. cordifolia fruits extracts and also the toxicity profile of the fruit should be essential for the future studies dealing with the long term effect in animals. © 2015 Wiley Periodicals, Inc. Environ Toxicol 31: 1059-1067, 2016. PMID:25926096

  12. Transformation Time

    ERIC Educational Resources Information Center

    Berry, John N., III

    2007-01-01

    The program for the march by librarians on America's capital for the American Library Association (ALA) conference is predictably loaded with lobbying, legislation, and DC tours. It also abounds with professional opportunity and reflects the impact of Leslie Burger, one of the most activist ALA presidents in recent history. Her "Transformation"…

  13. Transformation & Metamorphosis

    ERIC Educational Resources Information Center

    Lott, Debra

    2009-01-01

    The sculptures of Canadian artist Brian Jungen are a great inspiration for a lesson on creating new forms. Jungen transforms found objects into unique creations without fully concealing their original form or purpose. Frank Stella's sculpture series, including "K.132,2007" made of stainless steel and spray paint, is another great example of…

  14. Transforming Schools.

    ERIC Educational Resources Information Center

    Cookson, Peter W., Jr., Ed.; Schneider, Barbara, Ed.

    The authors in this book address the issues that relate to the crisis in American education and review some of the proposed solutions. To transform education, schools must be examined as social systems that are interrelated with families, communities, and the world of work. Following the introduction, section 1, "Conditions for Educational…

  15. Detecting patterns of protein distribution and gene expression in silico

    PubMed Central

    Geraghty, Michael T.; Bassett, Doug; Morrell, James C.; Gatto, Gregory J.; Bai, Jianwu; Geisbrecht, Brian V.; Hieter, Phil; Gould, Stephen J.

    1999-01-01

    Most biological information is contained within gene and genome sequences. However, current methods for analyzing these data are limited primarily to the prediction of coding regions and identification of sequence similarities. We have developed a computer algorithm, CoSMoS (for context sensitive motif searches), which adds context sensitivity to sequence motif searches. CoSMoS was challenged to identify genes encoding peroxisome-associated and oleate-induced genes in the yeast Saccharomyces cerevisiae. Specifically, we searched for genes capable of encoding proteins with a type 1 or type 2 peroxisomal targeting signal and for genes containing the oleate-response element, a cis-acting element common to fatty acid-regulated genes. CoSMoS successfully identified 7 of 8 known PTS-containing peroxisomal proteins and 13 of 14 known oleate-regulated genes. More importantly, CoSMoS identified an additional 18 candidate peroxisomal proteins and 300 candidate oleate-regulated genes. Preliminary localization studies suggest that these include at least 10 previously unknown peroxisomal proteins. Phenotypic studies of selected gene disruption mutants suggests that several of these new peroxisomal proteins play roles in growth on fatty acids, one is involved in peroxisome biogenesis and at least two are required for synthesis of lysine, a heretofore unrecognized role for peroxisomes. These results expand our understanding of peroxisome content and function, demonstrate the utility of CoSMoS for context-sensitive motif scanning, and point to the benefits of improved in silico genome analysis. PMID:10077615

  16. In Silico Reconstitution of Listeria Propulsion Exhibits Nano-Saltation

    PubMed Central

    2004-01-01

    To understand how the actin-polymerization-mediated movements in cells emerge from myriad individual protein–protein interactions, we developed a computational model of Listeria monocytogenes propulsion that explicitly simulates a large number of monomer-scale biochemical and mechanical interactions. The literature on actin networks and L. monocytogenes motility provides the foundation for a realistic mathematical/computer simulation, because most of the key rate constants governing actin network dynamics have been measured. We use a cluster of 80 Linux processors and our own suite of simulation and analysis software to characterize salient features of bacterial motion. Our “in silico reconstitution” produces qualitatively realistic bacterial motion with regard to speed and persistence of motion and actin tail morphology. The model also produces smaller scale emergent behavior; we demonstrate how the observed nano-saltatory motion of L. monocytogenes, in which runs punctuate pauses, can emerge from a cooperative binding and breaking of attachments between actin filaments and the bacterium. We describe our modeling methodology in detail, as it is likely to be useful for understanding any subcellular system in which the dynamics of many simple interactions lead to complex emergent behavior, e.g., lamellipodia and filopodia extension, cellular organization, and cytokinesis. PMID:15562315

  17. in silico Surveillance: evaluating outbreak detection with simulation models

    PubMed Central

    2013-01-01

    Background Detecting outbreaks is a crucial task for public health officials, yet gaps remain in the systematic evaluation of outbreak detection protocols. The authors’ objectives were to design, implement, and test a flexible methodology for generating detailed synthetic surveillance data that provides realistic geographical and temporal clustering of cases and use to evaluate outbreak detection protocols. Methods A detailed representation of the Boston area was constructed, based on data about individuals, locations, and activity patterns. Influenza-like illness (ILI) transmission was simulated, producing 100 years of in silico ILI data. Six different surveillance systems were designed and developed using gathered cases from the simulated disease data. Performance was measured by inserting test outbreaks into the surveillance streams and analyzing the likelihood and timeliness of detection. Results Detection of outbreaks varied from 21% to 95%. Increased coverage did not linearly improve detection probability for all surveillance systems. Relaxing the decision threshold for signaling outbreaks greatly increased false-positives, improved outbreak detection slightly, and led to earlier outbreak detection. Conclusions Geographical distribution can be more important than coverage level. Detailed simulations of infectious disease transmission can be configured to represent nearly any conceivable scenario. They are a powerful tool for evaluating the performance of surveillance systems and methods used for outbreak detection. PMID:23343523

  18. Integrating in silico resources to map a signaling network.

    PubMed

    Liu, Hanqing; Beck, Tim N; Golemis, Erica A; Serebriiskii, Ilya G

    2014-01-01

    The abundance of publicly available life science databases offers a wealth of information that can support interpretation of experimentally derived data and greatly enhance hypothesis generation. Protein interaction and functional networks are not simply new renditions of existing data: they provide the opportunity to gain insights into the specific physical and functional role a protein plays as part of the biological system. In this chapter, we describe different in silico tools that can quickly and conveniently retrieve data from existing data repositories and we discuss how the available tools are best utilized for different purposes. While emphasizing protein-protein interaction databases (e.g., BioGrid and IntAct), we also introduce metasearch platforms such as STRING and GeneMANIA, pathway databases (e.g., BioCarta and Pathway Commons), text mining approaches (e.g., PubMed and Chilibot), and resources for drug-protein interactions, genetic information for model organisms and gene expression information based on microarray data mining. Furthermore, we provide a simple step-by-step protocol for building customized protein-protein interaction networks in Cytoscape, a powerful network assembly and visualization program, integrating data retrieved from these various databases. As we illustrate, generation of composite interaction networks enables investigators to extract significantly more information about a given biological system than utilization of a single database or sole reliance on primary literature. PMID:24233784

  19. Pharmacokinetic properties and in silico ADME modeling in drug discovery.

    PubMed

    Honório, Kathia M; Moda, Tiago L; Andricopulo, Adriano D

    2013-03-01

    The discovery and development of a new drug are time-consuming, difficult and expensive. This complex process has evolved from classical methods into an integration of modern technologies and innovative strategies addressed to the design of new chemical entities to treat a variety of diseases. The development of new drug candidates is often limited by initial compounds lacking reasonable chemical and biological properties for further lead optimization. Huge libraries of compounds are frequently selected for biological screening using a variety of techniques and standard models to assess potency, affinity and selectivity. In this context, it is very important to study the pharmacokinetic profile of the compounds under investigation. Recent advances have been made in the collection of data and the development of models to assess and predict pharmacokinetic properties (ADME--absorption, distribution, metabolism and excretion) of bioactive compounds in the early stages of drug discovery projects. This paper provides a brief perspective on the evolution of in silico ADME tools, addressing challenges, limitations, and opportunities in medicinal chemistry. PMID:23016542

  20. Toward Fully in Silico Melting Point Prediction Using Molecular Simulations

    SciTech Connect

    Zhang, Y; Maginn, EJ

    2013-03-01

    Melting point is one of the most fundamental and practically important properties of a compound. Molecular computation of melting points. However, all of these methods simulation methods have been developed for the accurate need an experimental crystal structure as input, which means that such calculations are not really predictive since the melting point can be measured easily in experiments once a crystal structure is known. On the other hand, crystal structure prediction (CSP) has become an active field and significant progress has been made, although challenges still exist. One of the main challenges is the existence of many crystal structures (polymorphs) that are very close in energy. Thermal effects and kinetic factors make the situation even more complicated, such that it is still not trivial to predict experimental crystal structures. In this work, we exploit the fact that free energy differences are often small between crystal structures. We show that accurate melting point predictions can be made by using a reasonable crystal structure from CSP as a starting point for a free energy-based melting point calculation. The key is that most crystal structures predicted by CSP have free energies that are close to that of the experimental structure. The proposed method was tested on two rigid molecules and the results suggest that a fully in silico melting point prediction method is possible.

  1. A web portal for in-silico action potential predictions

    PubMed Central

    Williams, Geoff; Mirams, Gary R.

    2015-01-01

    Introduction Multiple cardiac ion channels are prone to block by pharmaceutical compounds, and this can have large implications for cardiac safety. The effect of a compound on individual ion currents can now be measured in automated patch clamp screening assays. In-silico action potential models are proposed as one way of predicting the integrated compound effects on whole-cell electrophysiology, to provide an improved indication of pro-arrhythmic risk. Methods We have developed open source software to run cardiac electrophysiology simulations to predict the overall effect of compounds that block IKr, ICaL, INa, IKs, IK1 and Ito to varying degrees, using a choice of mathematical electrophysiology models. To enable safety pharmacology teams to run and evaluate these simulations easily, we have also developed an open source web portal interface to this simulator. Results The web portal can be found at https://chaste.cs.ox.ac.uk/ActionPotential. Users can enter details of compound affinities for ion channels in the form of IC50 or pIC50 values, run simulations, store the results for later retrieval, view summary graphs of the results, and export data to a spreadsheet format. Discussion This web portal provides a simple interface to reference versions of mathematical models, and well-tested state-of-the-art equation solvers. It provides safety teams easy access to the emerging technology of cardiac electrophysiology simulations for use in the drug-discovery process. PMID:25963830

  2. Integrating In Silico Resources to Map a Signaling Network

    PubMed Central

    Liu, Hanqing; Beck, Tim N.; Golemis, Erica A.; Serebriiskii, Ilya G.

    2013-01-01

    The abundance of publicly available life science databases offer a wealth of information that can support interpretation of experimentally derived data and greatly enhance hypothesis generation. Protein interaction and functional networks are not simply new renditions of existing data: they provide the opportunity to gain insights into the specific physical and functional role a protein plays as part of the biological system. In this chapter, we describe different in silico tools that can quickly and conveniently retrieve data from existing data repositories and discuss how the available tools are best utilized for different purposes. While emphasizing protein-protein interaction databases (e.g., BioGrid and IntAct), we also introduce metasearch platforms such as STRING and GeneMANIA, pathway databases (e.g., BioCarta and Pathway Commons), text mining approaches (e.g., PubMed and Chilibot), and resources for drug-protein interactions, genetic information for model organisms and gene expression information based on microarray data mining. Furthermore, we provide a simple step-by-step protocol to building customized protein-protein interaction networks in Cytoscape, a powerful network assembly and visualization program, integrating data retrieved from these various databases. As we illustrate, generation of composite interaction networks enables investigators to extract significantly more information about a given biological system than utilization of a single database or sole reliance on primary literature. PMID:24233784

  3. In silico ionomics segregates parasitic from free-living eukaryotes.

    PubMed

    Greganova, Eva; Steinmann, Michael; Mäser, Pascal; Fankhauser, Niklaus

    2013-01-01

    Ion transporters are fundamental to life. Due to their ancient origin and conservation in sequence, ion transporters are also particularly well suited for comparative genomics of distantly related species. Here, we perform genome-wide ion transporter profiling as a basis for comparative genomics of eukaryotes. From a given predicted proteome, we identify all bona fide ion channels, ion porters, and ion pumps. Concentrating on unicellular eukaryotes (n = 37), we demonstrate that clustering of species according to their repertoire of ion transporters segregates obligate endoparasites (n = 23) on the one hand, from free-living species and facultative parasites (n = 14) on the other hand. This surprising finding indicates strong convergent evolution of the parasites regarding the acquisition and homeostasis of inorganic ions. Random forest classification identifies transporters of ammonia, plus transporters of iron and other transition metals, as the most informative for distinguishing the obligate parasites. Thus, in silico ionomics further underscores the importance of iron in infection biology and suggests access to host sources of nitrogen and transition metals to be selective forces in the evolution of parasitism. This finding is in agreement with the phenomenon of iron withholding as a primordial antimicrobial strategy of infected mammals. PMID:24048281

  4. In silico evolution of oscillatory dynamics in biochemical networks

    NASA Astrophysics Data System (ADS)

    Ali, Md Zulfikar; Wingreen, Ned S.; Mukhopadhyay, Ranjan

    2015-03-01

    We are studying in silico evolution of complex, oscillatory network dynamics within the framework of a minimal mutational model of protein-protein interactions. In our model we consider two different types of proteins, kinase (activator) and phosphatase(inhibitor). In our model. each protein can either be phosphorylated(active) or unphospphorylated (inactive), represented by binary strings. Active proteins can modify their target based on the Michaelis-Menten kinetics of chemical equation. Reaction rate constants are directly related to sequence dependent protein-protein interaction energies. This model can be stuided for non-trivial behavior e.g. oscillations, chaos, multiple stable states. We focus here on biochemical oscillators; some questions we will address within our framework include how the oscillatory dynamics depends on number of protein species, connectivity of the network, whether evolution can readily converge on a stable oscillator if we start with random intitial parameters, neutral evolution with additional protein components and general questions of robustness and evolavability.

  5. In Silico Ionomics Segregates Parasitic from Free-Living Eukaryotes

    PubMed Central

    Greganova, Eva; Steinmann, Michael; Mäser, Pascal; Fankhauser, Niklaus

    2013-01-01

    Ion transporters are fundamental to life. Due to their ancient origin and conservation in sequence, ion transporters are also particularly well suited for comparative genomics of distantly related species. Here, we perform genome-wide ion transporter profiling as a basis for comparative genomics of eukaryotes. From a given predicted proteome, we identify all bona fide ion channels, ion porters, and ion pumps. Concentrating on unicellular eukaryotes (n = 37), we demonstrate that clustering of species according to their repertoire of ion transporters segregates obligate endoparasites (n = 23) on the one hand, from free-living species and facultative parasites (n = 14) on the other hand. This surprising finding indicates strong convergent evolution of the parasites regarding the acquisition and homeostasis of inorganic ions. Random forest classification identifies transporters of ammonia, plus transporters of iron and other transition metals, as the most informative for distinguishing the obligate parasites. Thus, in silico ionomics further underscores the importance of iron in infection biology and suggests access to host sources of nitrogen and transition metals to be selective forces in the evolution of parasitism. This finding is in agreement with the phenomenon of iron withholding as a primordial antimicrobial strategy of infected mammals. PMID:24048281

  6. In silico antitubercular activity analysis of benzofuran and naphthofuran derivatives.

    PubMed

    Karunakar, Prashantha; Girija, Chamarahalli Ramakrishnaiyer; Krishnamurthy, Venkatappa; Krishna, Venkatarangaiah; Shivakumar, Kunigal Venugopal

    2014-01-01

    For the human health, Mycobacterium tuberculosis (MTB) is the deadliest enemy since decades due to its multidrug resistant strains. During latent stage of tuberculosis infection, MTB consumes nitrate as the alternate mechanism of respiration in the absence of oxygen, thus increasing its survival and virulence. NarL is a nitrate/nitrite response transcriptional regulatory protein of two-component signal transduction system which regulates nitrate reductase and formate dehydrogenase for MTB adaptation to anaerobic condition. Phosphorylation by sensor kinase (NarX) is the primary mechanism behind the activation of NarL although many response regulators get activated by small molecule phospho-donors in the absence of sensor kinase. Using in silico approach, the molecular docking of benzofuran and naphthofuran derivatives and dynamic study of benzofuran derivative were performed. It was observed that compound Ethyl 5-bromo-3-ethoxycarbonylamino-1-benzofuran-2-carboxylate could be stabilized at the active site for over 10 ns of simulation. Here we suggest that derivatives of benzofuran moiety can lead to developing novel antituberculosis drugs. PMID:25302118

  7. Characterization of forced degradation products of pazopanib hydrochloride by UHPLC-Q-TOF/MS and in silico toxicity prediction.

    PubMed

    Patel, Prinesh N; Kalariya, Pradipbhai D; Sharma, Mahesh; Garg, Prabha; Talluri, M V N Kumar; Gananadhamu, S; Srinivas, R

    2015-07-01

    Pazopanib (PZ), an anti-cancer drug, was subjected to forced degradation under hydrolytic (acid, base and neutral), oxidative, photolytic and thermal stress conditions as per International Conference on Harmonization guidelines. A selective stability indicating validated method was developed using a Waters Acquity UPLC HSS T3 (100 × 2.1 mm, 1.7 µm) column in gradient mode with ammonium acetate buffer (10 mM, pH 5.0) and acetonitrile. PZ was found to degrade only in photolytic conditions to produce six transformation products (TPs). All the TPs were identified and characterized by liquid chromatography/atmospheric pressure chemical ionization-quadrupole-time of flight mass spectrometry experiments in combination with accurate mass measurements. Plausible mechanisms have been proposed for the formation of TPs. In silico toxicity was predicted using TOPKAT and DEREK softwares for all the TPs. The TP, N4-(2,3-dimethyl-2H-indazol-6-yl)-N4-methylpyrimidine-2,4-diamine, was found to be genotoxic, whereas all other TPs with sulfonamide moiety were hepatotoxic. The data reported here are expected to be of significance as this study foresees the formation of one potential genotoxic and five hepatotoxic degradation/transformation products. PMID:26349647

  8. In silico analysis of stomach lineage specific gene set expression pattern in gastric cancer

    SciTech Connect

    Pandi, Narayanan Sathiya Suganya, Sivagurunathan; Rajendran, Suriliyandi

    2013-10-04

    Highlights: •Identified stomach lineage specific gene set (SLSGS) was found to be under expressed in gastric tumors. •Elevated expression of SLSGS in gastric tumor is a molecular predictor of metabolic type gastric cancer. •In silico pathway scanning identified estrogen-α signaling is a putative regulator of SLSGS in gastric cancer. •Elevated expression of SLSGS in GC is associated with an overall increase in the survival of GC patients. -- Abstract: Stomach lineage specific gene products act as a protective barrier in the normal stomach and their expression maintains the normal physiological processes, cellular integrity and morphology of the gastric wall. However, the regulation of stomach lineage specific genes in gastric cancer (GC) is far less clear. In the present study, we sought to investigate the role and regulation of stomach lineage specific gene set (SLSGS) in GC. SLSGS was identified by comparing the mRNA expression profiles of normal stomach tissue with other organ tissue. The obtained SLSGS was found to be under expressed in gastric tumors. Functional annotation analysis revealed that the SLSGS was enriched for digestive function and gastric epithelial maintenance. Employing a single sample prediction method across GC mRNA expression profiles identified the under expression of SLSGS in proliferative type and invasive type gastric tumors compared to the metabolic type gastric tumors. Integrative pathway activation prediction analysis revealed a close association between estrogen-α signaling and SLSGS expression pattern in GC. Elevated expression of SLSGS in GC is associated with an overall increase in the survival of GC patients. In conclusion, our results highlight that estrogen mediated regulation of SLSGS in gastric tumor is a molecular predictor of metabolic type GC and prognostic factor in GC.

  9. Genetic analysis, in silico prediction, and family segregation in long QT syndrome.

    PubMed

    Riuró, Helena; Campuzano, Oscar; Berne, Paola; Arbelo, Elena; Iglesias, Anna; Pérez-Serra, Alexandra; Coll-Vidal, Mònica; Partemi, Sara; Mademont-Soler, Irene; Picó, Ferran; Allegue, Catarina; Oliva, Antonio; Gerstenfeld, Edward; Sarquella-Brugada, Georgia; Castro-Urda, Víctor; Fernández-Lozano, Ignacio; Mont, Lluís; Brugada, Josep; Scornik, Fabiana S; Brugada, Ramon

    2015-01-01

    The heritable cardiovascular disorder long QT syndrome (LQTS), characterized by prolongation of the QT interval on electrocardiogram, carries a high risk of sudden cardiac death. We sought to add new data to the existing knowledge of genetic mutations contributing to LQTS to both expand our understanding of its genetic basis and assess the value of genetic testing in clinical decision-making. Direct sequencing of the five major contributing genes, KCNQ1, KCNH2, SCN5A, KCNE1, and KCNE2, was performed in a cohort of 115 non-related LQTS patients. Pathogenicity of the variants was analyzed using family segregation, allele frequency from public databases, conservation analysis, and Condel and Provean in silico predictors. Phenotype-genotype correlations were analyzed statistically. Sequencing identified 36 previously described and 18 novel mutations. In 51.3% of the index cases, mutations were found, mostly in KCNQ1, KCNH2, and SCN5A; 5.2% of cases had multiple mutations. Pathogenicity analysis revealed 39 mutations as likely pathogenic, 12 as VUS, and 3 as non-pathogenic. Clinical analysis revealed that 75.6% of patients with QTc≥500 ms were genetically confirmed. Our results support the use of genetic testing of KCNQ1, KCNH2, and SCN5A as part of the diagnosis of LQTS and to help identify relatives at risk of SCD. Further, the genetic tools appear more valuable as disease severity increases. However, the identification of genetic variations in the clinical investigation of single patients using bioinformatic tools can produce erroneous conclusions regarding pathogenicity. Therefore segregation studies are key to determining causality. PMID:24667783

  10. Polyelectrolyte complex of vancomycin as a nanoantibiotic: Preparation, in vitro and in silico studies.

    PubMed

    Sikwal, Dhiraj R; Kalhapure, Rahul S; Rambharose, Sanjeev; Vepuri, Suresh; Soliman, Mahmoud; Mocktar, Chunderika; Govender, Thirumala

    2016-06-01

    Delivery of antibiotics by various nanosized carriers is proving to be a promising strategy to combat limitations associated with conventional dosage forms and the ever-increasing drug resistance problem. This method entails improving the pharmacokinetic parameters for accumulation at the target infection site and reducing their adverse effects. It has been proposed that antibiotic nanoparticles themselves are more effective delivery system than encapsulating the antibiotic in a nanosystem. In this study, we report on nanoparticles of vancomycin (VCM) by self-assembled amphiphilic-polyelectrolyte complexation between VCM hydrochloride and polyacrylic acid sodium (PAA). The size, polydispersity index and zeta potential of the developed nanoplexes were 229.7±47.76nm, 0.442±0.075, -30.4±5.3mV respectively, whereas complexation efficiency, drug loading and percentage yield were 75.22±1.02%, 58.40±1.03% and 60.60±2.62% respectively. An in vitro cytotoxicity study on three mammalian cell lines using MTT assays confirmed the biosafety of the newly formulated nanoplexes. Morphological investigations using scanning electron microscope showed cube shaped hexagonal-like particles. In vitro drug release studies revealed that the drug was completely released from the nanoplexes within 12h. In silico studies revealed that the nano-aggregation was facilitated by means of self-association of VCM in the presence of the polymer. The supramolecular pattern of the drug self-association was found to be similar to that of the VCM dimer observed in the crystal structure of the VCM available in Protein Data Bank. In vitro antibacterial activity against susceptible and resistant Staphylococcus aureus proved that the potency of VCM was retained after being formulated as the nanoplex. In conclusion, VCM nanoplexes could be a promising nanodrug delivery system to treat infections of S. aureus origin. PMID:27040243

  11. Genetic analysis, in silico prediction, and family segregation in long QT syndrome

    PubMed Central

    Riuró, Helena; Campuzano, Oscar; Berne, Paola; Arbelo, Elena; Iglesias, Anna; Pérez-Serra, Alexandra; Coll-Vidal, Mònica; Partemi, Sara; Mademont-Soler, Irene; Picó, Ferran; Allegue, Catarina; Oliva, Antonio; Gerstenfeld, Edward; Sarquella-Brugada, Georgia; Castro-Urda, Víctor; Fernández-Lozano, Ignacio; Mont, Lluís; Brugada, Josep; Scornik, Fabiana S; Brugada, Ramon

    2015-01-01

    The heritable cardiovascular disorder long QT syndrome (LQTS), characterized by prolongation of the QT interval on electrocardiogram, carries a high risk of sudden cardiac death. We sought to add new data to the existing knowledge of genetic mutations contributing to LQTS to both expand our understanding of its genetic basis and assess the value of genetic testing in clinical decision-making. Direct sequencing of the five major contributing genes, KCNQ1, KCNH2, SCN5A, KCNE1, and KCNE2, was performed in a cohort of 115 non-related LQTS patients. Pathogenicity of the variants was analyzed using family segregation, allele frequency from public databases, conservation analysis, and Condel and Provean in silico predictors. Phenotype-genotype correlations were analyzed statistically. Sequencing identified 36 previously described and 18 novel mutations. In 51.3% of the index cases, mutations were found, mostly in KCNQ1, KCNH2, and SCN5A; 5.2% of cases had multiple mutations. Pathogenicity analysis revealed 39 mutations as likely pathogenic, 12 as VUS, and 3 as non-pathogenic. Clinical analysis revealed that 75.6% of patients with QTc≥500 ms were genetically confirmed. Our results support the use of genetic testing of KCNQ1, KCNH2, and SCN5A as part of the diagnosis of LQTS and to help identify relatives at risk of SCD. Further, the genetic tools appear more valuable as disease severity increases. However, the identification of genetic variations in the clinical investigation of single patients using bioinformatic tools can produce erroneous conclusions regarding pathogenicity. Therefore segregation studies are key to determining causality. PMID:24667783

  12. Using proteomic data to assess a genome-scale "in silico" model of metal reducing bacteria in the simulation of field-scale uranium bioremediation

    NASA Astrophysics Data System (ADS)

    Yabusaki, S.; Fang, Y.; Wilkins, M. J.; Long, P.; Rifle IFRC Science Team

    2011-12-01

    citrate synthase that generates citrate from acetyl-CoA and oxaloacetate). Model discrepancies with the proteomic data, such as the prediction of shifts associated with nitrogen limitation, revealed pathways in the in silico code that could be modified to more accurately predict metabolic processes that occur in the subsurface. The potential outcome of this approach is the engineering of electron donor (e.g., acetate), terminal electron acceptor [e.g., U(VI)], and biogeochemical conditions that enhance the desired metabolic pathways of the target microorganism(s) to effect cost-effective uranium bioreduction.

  13. STEM Career Changers' Transformation into Science Teachers

    ERIC Educational Resources Information Center

    Snyder, Catherine; Oliveira, Alandeom W.; Paska, Lawrence M.

    2013-01-01

    This study examines the transformation (professional growth) of career-changing women scientists who decided to become teachers. Drawing upon Mezirow's Transformative Learning Theory, we tracked their transformation for 3 years. Our findings revealed multiple identities, disorientation, a perceived sense of meaninglessness, loss and eventual…

  14. The Use of Transformations in Solving Equations

    ERIC Educational Resources Information Center

    Libeskind, Shlomo

    2010-01-01

    Many workshops and meetings with the US high school mathematics teachers revealed a lack of familiarity with the use of transformations in solving equations and problems related to the roots of polynomials. This note describes two transformational approaches to the derivation of the quadratic formula as well as transformational approaches to…

  15. Aquatic photochemistry, abiotic and aerobic biodegradability of thalidomide: identification of stable transformation products by LC-UV-MS(n).

    PubMed

    Mahmoud, Waleed M M; Trautwein, Christoph; Leder, Christoph; Kümmerer, Klaus

    2013-10-01

    Thalidomide (TD), besides being notorious for its teratogenicity, was shown to have immunomodulating and anti-inflammatory activities. This is why recently TD became a promising drug for the treatment of different cancers and inflammatory diseases. Yet nothing is known about the environmental fate of TD, which therefore was assessed experimentally and by in silico prediction programs (quantitative structure activity relationship (QSAR) models) within this study. Photolytic degradation was tested with two different light sources (medium-pressure mercury lamp; xenon lamp) and aerobic biodegradability was investigated with two OECD tests (Closed Bottle test (CBT), Manometric Respirometry test (MRT)). An additional CBT was performed for TD samples after 16 min of UV-photolysis. The primary elimination of TD was monitored and the structures of its photo-, abiotic and biodegradation products were elucidated by HPLC-UV-Fluorescence-MS(n). Furthermore, elimination of dissolved organic carbon was monitored in the photolysis experiment. LC-MS revealed that new photolytic transformation products (TPs) were identified, among them two isomers of TD with the same molecular mass. These TPs were different to the products formed by biodegradation. The experimental findings were compared with the results obtained from the in silico prediction programs where e.g. a good correlation for TD biodegradation in the CBT was confirmed. Moreover, some of the identified TPs were also structurally predicted by the MetaPC software. These results demonstrate that TD and its TPs are not readily biodegradable and not fully mineralized by photochemical treatment. They may therefore pose a risk to the aquatic environment due to the pharmacological activity of TD and unknown properties of its TPs. The applied techniques within this study emphasize the importance of QSAR models as a tool for estimating environmental risk assessments. PMID:23792256

  16. MicroRNA miR-146a and further oncogenesis-related cellular microRNAs are dysregulated in HTLV-1-transformed T lymphocytes

    PubMed Central

    Pichler, Klemens; Schneider, Grit; Grassmann, Ralph

    2008-01-01

    Background Human T-lymphotropic virus type 1 (HTLV-1) is the etiologic agent of a severe and fatal lymphoproliferative disease of mainly CD4+ T cell origin, adult T cell leukemia, which develops after prolonged viral persistence. Transformation of infected cells involves HTLV-1's oncoprotein Tax, which perturbs cell cycle regulation and modulates cellular gene expression. The latter function is also a hallmark of microRNAs, a rather new layer in the regulation of gene expression. Affecting e.g. proliferation, microRNAs constitute a potential target for viral interference on the way to persistence and transformation. Hence, we explored the interconnections between HTLV-1 and cellular microRNAs. Results We report that several microRNAs – miRs 21, 24, 146a, 155 and 223 – are deregulated in HTLV-1-transformed cells. They are all upregulated except for miR-223, which is downregulated. Each of those microRNAs has ties to cancer. Their expression pattern forms a uniform phenotype among HTLV-transformed cells when compared to HTLV-negative control cells. In particular, miR-146a expression was found to be directly stimulated by Tax via NF-κB-mediated transactivation of its promoter; a single NF-κB site proximal to the transcription start point was necessary and sufficient for this to happen. An in silico analysis of potential target genes revealed candidates that might be coregulated by two or more of the aforementioned overexpressed microRNAs. Conclusion These data demonstrate that cellular microRNAs are deregulated in HTLV-1-transformed T cells. In the case of miR-146a, this could be directly attributed to HTLV's oncoprotein Tax. Interference with cellular microRNAs may be crucial to maintaining persistence or may facilitate transformation of host cells. PMID:19014482

  17. Revealing ontological commitments by magic.

    PubMed

    Griffiths, Thomas L

    2015-03-01

    Considering the appeal of different magical transformations exposes some systematic asymmetries. For example, it is more interesting to transform a vase into a rose than a rose into a vase. An experiment in which people judged how interesting they found different magic tricks showed that these asymmetries reflect the direction a transformation moves in an ontological hierarchy: transformations in the direction of animacy and intelligence are favored over the opposite. A second and third experiment demonstrated that judgments of the plausibility of machines that perform the same transformations do not show the same asymmetries, but judgments of the interestingness of such machines do. A formal argument relates this sense of interestingness to evidence for an alternative to our current physical theory, with magic tricks being a particularly pure source of such evidence. These results suggest that people's intuitions about magic tricks can reveal the ontological commitments that underlie human cognition. PMID:25490128

  18. METABOLISM AND METABOLIC ACTIVATION OF CHEMICALS: IN-SILICO SIMULATION

    EPA Science Inventory

    The role of metabolism in prioritizing chemicals according to their potential adverse health effects is extremely important because innocuous parents can be transformed into toxic metabolites. This work presents the TIssue MEtabolism Simulator (TIMES) platform for simulating met...

  19. RF transformer

    DOEpatents

    Smith, James L.; Helenberg, Harold W.; Kilsdonk, Dennis J.

    1979-01-01

    There is provided an improved RF transformer having a single-turn secondary of cylindrical shape and a coiled encapsulated primary contained within the secondary. The coil is tapered so that the narrowest separation between the primary and the secondary is at one end of the coil. The encapsulated primary is removable from the secondary so that a variety of different capacity primaries can be utilized with one secondary.

  20. In vitro and in silico modeling of chromosomal instability

    NASA Astrophysics Data System (ADS)

    Andreev, Sergey; Eidelman, Yuri; Krasavin, Eugene; Govorun, Raisa; Koshlan, Igor; Pyatenko, Valentina; Korovchuk, Olga; Khvostunov, Igor; Sevankaev, Alexander

    Exposure to ionizing radiation increases cancer risk in human population. Cancer is thought to originate from an altered expression of certain number of specific genes. It is widely recognized that chromosome aberrations (CA) are involved in stable change in expression of genes by gain or loss of their functions. Thus CA can contribute to initiation or progression of cancer. Radiation induces CA immediately after exposure (in first cell cycle) and results in formation of delayed CA in descendants of irradiated cells, or chromosomal instability phenotype (CI). Therefore quantification of CI is a prerequisite of any mechanistic model of radiation induced cancer risks. To quantify CI we designed a set of in vitr o and in silico experiments. Two experimental models for study of CI in vitro, CHO-K1 wild-type and V79 HPRT-mutant cells, were exploited. Chromosome and chromatid type aberrations (Giemsa staining) were scored following exposure to gamma-radiation and accelerated ions (protons, LET=0.22 keV/µm, 7 Li3+ , LET=20 keV/µm, 14 7+ N , LET=77 keV/µm). The obtained results suggested that slowly growing colonies of HPRT mutant cells originating from lowand high-LET irradiated wt V79 cells were formed. After 14 N7+ ions irradiation about 50-100% of colonies had the decreased growth rate and CI phenotype was observed mainly in slowly growing colonies. High, compared to control, level of unstable CA (dicentrics) was observed in the progeny of gamma-irradiated CHO-K1 cells at different time points up to 30 cell generations. CA frequency, the number of cells with aberrations and the shape of a CA-vs-time curve were found to be dependent on the cell culture state (stationary or logarithmic phase) in which they were irradiated. Inhibition of replication and repair DNA synthesis by ara-C and hydroxyurea resulted in small modification of CA dynamics for stat-phase cells. For log-phase cell culture, in contrast, DNA synthesis inhibitors drastically impacted CA dynamics. In

  1. In silico analysis of nanomaterials hazard and risk.

    PubMed

    Cohen, Yoram; Rallo, Robert; Liu, Rong; Liu, Haoyang Haven

    2013-03-19

    Because a variety of human-related activities, engineer-ed nanoparticles (ENMs) may be released to various environmental media and may cross environmental boundaries, and thus will be found in most media. Therefore, the potential environmental impacts of ENMs must be assessed from a multimedia perspective and with an integrated risk management approach that considers rapid developments and increasing use of new nanomaterials. Accordingly, this Account presents a rational process for the integration of in silico ENM toxicity and fate and transport analyses for environmental impact assessment. This approach requires knowledge of ENM toxicity and environmental exposure concentrations. Considering the large number of current different types of ENMs and that those numbers are likely to increase, there is an urgent need to accelerate the evaluation of their toxicity and the assessment of their potential distribution in the environment. Developments in high throughput screening (HTS) are now enabling the rapid generation of large data sets for ENM toxicity assessment. However, these analyses require the establishment of reliable toxicity metrics, especially when HTS includes data from multiple assays, cell lines, or organisms. Establishing toxicity metrics with HTS data requires advanced data processing techniques in order to clearly identify significant biological effects associated with exposure to ENMs. HTS data can form the basis for developing and validating in silico toxicity models (e.g., quantitative structure-activity relationships) and for generating data-driven hypotheses to aid in establishing and/or validating possible toxicity mechanisms. To correlate the toxicity of ENMs with their physicochemical properties, researchers will need to develop quantitative structure-activity relationships for nanomaterials (i.e., nano-SARs). However, as nano-SARs are applied in regulatory applications, researchers must consider their applicability and the acceptance level of

  2. Solitons and protein folding: An In Silico experiment

    SciTech Connect

    Ilieva, N.; Dai, J.; Sieradzan, A.; Niemi, A.

    2015-10-28

    Protein folding [1] is the process of formation of a functional 3D structure from a random coil — the shape in which amino-acid chains leave the ribosome. Anfinsen’s dogma states that the native 3D shape of a protein is completely determined by protein’s amino acid sequence. Despite the progress in understanding the process rate and the success in folding prediction for some small proteins, with presently available physics-based methods it is not yet possible to reliably deduce the shape of a biologically active protein from its amino acid sequence. The protein-folding problem endures as one of the most important unresolved problems in science; it addresses the origin of life itself. Furthermore, a wrong fold is a common cause for a protein to lose its function or even endanger the living organism. Soliton solutions of a generalized discrete non-linear Schrödinger equation (GDNLSE) obtained from the energy function in terms of bond and torsion angles κ and τ provide a constructive theoretical framework for describing protein folds and folding patterns [2]. Here we study the dynamics of this process by means of molecular-dynamics simulations. The soliton manifestation is the pattern helix–loop–helix in the secondary structure of the protein, which explains the importance of understanding loop formation in helical proteins. We performed in silico experiments for unfolding one subunit of the core structure of gp41 from the HIV envelope glycoprotein (PDB ID: 1AIK [3]) by molecular-dynamics simulations with the MD package GROMACS. We analyzed 80 ns trajectories, obtained with one united-atom and two different all-atom force fields, to justify the side-chain orientation quantification scheme adopted in the studies and to eliminate force-field based artifacts. Our results are compatible with the soliton model of protein folding and provide first insight into soliton-formation dynamics.

  3. In silico predicted structural and functional robustness of piscine steroidogenesis.

    PubMed

    Hala, D; Huggett, D B

    2014-03-21

    Assessments of metabolic robustness or susceptibility are inherently dependent on quantitative descriptions of network structure and associated function. In this paper a stoichiometric model of piscine steroidogenesis was constructed and constrained with productions of selected steroid hormones. Structural and flux metrics of this in silico model were quantified by calculating extreme pathways and optimal flux distributions (using linear programming). Extreme pathway analysis showed progestin and corticosteroid synthesis reactions to be highly participant in extreme pathways. Furthermore, reaction participation in extreme pathways also fitted a power law distribution (degree exponent γ=2.3), which suggested that progestin and corticosteroid reactions act as 'hubs' capable of generating other functionally relevant pathways required to maintain steady-state functionality of the network. Analysis of cofactor usage (O2 and NADPH) showed progestin synthesis reactions to exhibit high robustness, whereas estrogen productions showed highest energetic demands with low associated robustness to maintain such demands. Linear programming calculated optimal flux distributions showed high heterogeneity of flux values with a near-random power law distribution (degree exponent γ≥2.7). Subsequently, network robustness was tested by assessing maintenance of metabolite flux-sum subject to targeted deletions of rank-ordered (low to high metric) extreme pathway participant and optimal flux reactions. Network robustness was susceptible to deletions of extreme pathway participant reactions, whereas minimal impact of high flux reaction deletion was observed. This analysis shows that the steroid network is susceptible to perturbation of structurally relevant (extreme pathway) reactions rather than those carrying high flux. PMID:24333207

  4. Solitons and protein folding: An In Silico experiment

    NASA Astrophysics Data System (ADS)

    Ilieva, N.; Dai, J.; Sieradzan, A.; Niemi, A.

    2015-10-01

    Protein folding [1] is the process of formation of a functional 3D structure from a random coil — the shape in which amino-acid chains leave the ribosome. Anfinsen's dogma states that the native 3D shape of a protein is completely determined by protein's amino acid sequence. Despite the progress in understanding the process rate and the success in folding prediction for some small proteins, with presently available physics-based methods it is not yet possible to reliably deduce the shape of a biologically active protein from its amino acid sequence. The protein-folding problem endures as one of the most important unresolved problems in science; it addresses the origin of life itself. Furthermore, a wrong fold is a common cause for a protein to lose its function or even endanger the living organism. Soliton solutions of a generalized discrete non-linear Schrödinger equation (GDNLSE) obtained from the energy function in terms of bond and torsion angles κ and τ provide a constructive theoretical framework for describing protein folds and folding patterns [2]. Here we study the dynamics of this process by means of molecular-dynamics simulations. The soliton manifestation is the pattern helix-loop-helix in the secondary structure of the protein, which explains the importance of understanding loop formation in helical proteins. We performed in silico experiments for unfolding one subunit of the core structure of gp41 from the HIV envelope glycoprotein (PDB ID: 1AIK [3]) by molecular-dynamics simulations with the MD package GROMACS. We analyzed 80 ns trajectories, obtained with one united-atom and two different all-atom force fields, to justify the side-chain orientation quantification scheme adopted in the studies and to eliminate force-field based artifacts. Our results are compatible with the soliton model of protein folding and provide first insight into soliton-formation dynamics.

  5. A Method for Accurate in silico modeling of Ultrasound Transducer Arrays

    PubMed Central

    Guenther, Drake A.; Walker, William F.

    2009-01-01

    This paper presents a new approach to improve the in silico modeling of ultrasound transducer arrays. While current simulation tools accurately predict the theoretical element spatio-temporal pressure response, transducers do not always behave as theorized. In practice, using the probe's physical dimensions and published specifications in silico, often results in unsatisfactory agreement between simulation and experiment. We describe a general optimization procedure used to maximize the correlation between the observed and simulated spatio-temporal response of a pulsed single element in a commercial ultrasound probe. A linear systems approach is employed to model element angular sensitivity, lens effects, and diffraction phenomena. A numerical deconvolution method is described to characterize the intrinsic electro-mechanical impulse response of the element. Once the response of the element and optimal element characteristics are known, prediction of the pressure response for arbitrary apertures and excitation signals is performed through direct convolution using available tools. We achieve a correlation of 0.846 between the experimental emitted waveform and simulated waveform when using the probe's physical specifications in silico. A far superior correlation of 0.988 is achieved when using the optimized in silico model. Electronic noise appears to be the main effect preventing the realization of higher correlation coefficients. More accurate in silico modeling will improve the evaluation and design of ultrasound transducers as well as aid in the development of sophisticated beamforming strategies. PMID:19041997

  6. In silico pharmacology for drug discovery: applications to targets and beyond

    PubMed Central

    Ekins, S; Mestres, J; Testa, B

    2007-01-01

    Computational (in silico) methods have been developed and widely applied to pharmacology hypothesis development and testing. These in silico methods include databases, quantitative structure-activity relationships, similarity searching, pharmacophores, homology models and other molecular modeling, machine learning, data mining, network analysis tools and data analysis tools that use a computer. Such methods have seen frequent use in the discovery and optimization of novel molecules with affinity to a target, the clarification of absorption, distribution, metabolism, excretion and toxicity properties as well as physicochemical characterization. The first part of this review discussed the methods that have been used for virtual ligand and target-based screening and profiling to predict biological activity. The aim of this second part of the review is to illustrate some of the varied applications of in silico methods for pharmacology in terms of the targets addressed. We will also discuss some of the advantages and disadvantages of in silico methods with respect to in vitro and in vivo methods for pharmacology research. Our conclusion is that the in silico pharmacology paradigm is ongoing and presents a rich array of opportunities that will assist in expediating the discovery of new targets, and ultimately lead to compounds with predicted biological activity for these novel targets. PMID:17549046

  7. The Consultancy Activity on In Silico Models for Genotoxic Prediction of Pharmaceutical Impurities.

    PubMed

    Pavan, Manuela; Kovarich, Simona; Bassan, Arianna; Broccardo, Lorenza; Yang, Chihae; Fioravanzo, Elena

    2016-01-01

    The toxicological assessment of DNA-reactive/mutagenic or clastogenic impurities plays an important role in the regulatory process for pharmaceuticals; in this context, in silico structure-based approaches are applied as primary tools for the evaluation of the mutagenic potential of the drug impurities. The general recommendations regarding such use of in silico methods are provided in the recent ICH M7 guideline stating that computational (in silico) toxicology assessment should be performed using two (Q)SAR prediction methodologies complementing each other: a statistical-based method and an expert rule-based method.Based on our consultant experience, we describe here a framework for in silico assessment of mutagenic potential of drug impurities. Two main applications of in silico methods are presented: (1) support and optimization of drug synthesis processes by providing early indication of potential genotoxic impurities and (2) regulatory evaluation of genotoxic potential of impurities in compliance with the ICH M7 guideline. Some critical case studies are also discussed. PMID:27311479

  8. Uptake of Host Cell Transforming Growth Factor-β by Trypanosoma cruzi Amastigotes in Cardiomyocytes

    PubMed Central

    Waghabi, Mariana C.; Keramidas, Michelle; Bailly, Sabine; Degrave, Wim; Mendonça-Lima, Leila; Soeiro, Maria de Nazaré C.; Meirelles, Maria de Nazareth L.; Paciornik, Sidnei; Araújo-Jorge, Tania C.; Feige, Jean-Jacques

    2005-01-01

    The cytokine transforming growth factor-β (TGF-β) plays various functions in the control of Trypanosoma cruzi infectivity and in the progression of Chagas’ disease. When we immunostained T. cruzi-infected cardiomyocytes (after either in vivo or in vitro infections) for TGF-β, we observed stronger immunoreactivity in parasites than in host cells. TGF-β immunoreactivity evolved during parasite cycle progression, with intense staining in amastigotes versus very faint staining in trypomastigotes. TGF-β was present on the surface of amastigotes, in the flagellar pocket, and in intraparasitic vesicles as revealed by electron microscopy. However, no ortholog TGF-β gene could be identified in the genome of T. cruzi by in silico analysis or by extensive polymerase chain reaction and reverse transcriptase-polymerase chain reaction studies. Immunoreactive TGF-β was most probably taken up by the parasite from the host cell cytoplasm because such an internalization process of biotinylated TGF-β could be observed in axenic amastigotes in vitro. These observations represent the first example of a novel mechanism by which a primitive unicellular protozoan can use host cell TGF-β to control its own intracellular life cycle. PMID:16192635

  9. SIRT1 contributes to aldose reductase expression through modulating NFAT5 under osmotic stress: In vitro and in silico insights.

    PubMed

    Timucin, Ahmet Can; Bodur, Cagri; Basaga, Huveyda

    2015-11-01

    So far, a myriad of molecules were characterized to modulate NFAT5 and its downstream targets. Among these NFAT5 modifiers, SIRT1 was proposed to have a promising role in NFAT5 dependent events, yet the exact underlying mechanism still remains obscure. Hence, the link between SIRT1 and NFAT5-aldose reductase (AR) axis under osmotic stress, was aimed to be delineated in this study. A unique osmotic stress model was generated and its mechanistic components were deciphered in U937 monocytes. In this model, AR expression and nuclear NFAT5 stabilization were revealed to be positively regulated by SIRT1 through utilization of pharmacological modulators. Overexpression and co-transfection studies of NFAT5 and SIRT1 further validated the contribution of SIRT1 to AR and NFAT5. The involvement of SIRT1 activity in these events was mediated via modification of DNA binding of NFAT5 to AR ORE region. Besides, NFAT5 and SIRT1 were also shown to co-immunoprecipitate under isosmotic conditions and this interaction was disrupted by osmotic stress. Further in silico experiments were conducted to investigate if SIRT1 directly targets NFAT5. In this regard, certain lysine residues of NFAT5, when kept deacetylated, were found to contribute to its DNA binding and SIRT1 was shown to directly bind K282 of NFAT5. Based on these in vitro and in silico findings, SIRT1 was identified, for the first time, as a novel positive regulator of NFAT5 dependent AR expression under osmotic stress in U937 monocytes. PMID:26297866

  10. In silico prediction and validation of potential gene targets for pospiviroid-derived small RNAs during tomato infection.

    PubMed

    Avina-Padilla, Katia; Martinez de la Vega, Octavio; Rivera-Bustamante, Rafael; Martinez-Soriano, Juan Pablo; Owens, Robert A; Hammond, Rosemarie W; Vielle-Calzada, Jean-Philippe

    2015-06-15

    Viroids are small, covalently closed, circular non-coding RNA pathogens of flowering plants. It is proposed that the symptoms of viroid pathogenesis result from a direct interaction between the viroid genomic RNA and unknown host plant factors. Using a comparative genomic approach we took advantage of the detailed annotation of the Arabidopsis thaliana (Arabidopsis) genome to identify sequence homologies between putative viroid-derived small RNAs (vd-sRNAs) and coding regions in the plant genome. A pool of sequence homologies among 29 species of the Pospiviroidae family and the Arabidopsis genome was analyzed. Using this strategy we identified putative host gene targets that may be involved in symptom expression in viroid-infected plants. In this communication, we report the in silico prediction and the experimental validation of pospiviroid-derived sRNAs conserved in the lower strand of the pathogenicity domain of seven viroid species infecting tomato; those vd-sRNAs targeted for cleavage the host mRNA encoding a conserved tomato WD40-repeat protein (SolWD40-repeat; SGN_U563134). Analysis of SolWD40-repeat expression indicated that this gene is down-regulated in tomato plants infected with tomato planta macho viroid (TPMVd). Furthermore, 5' RLM-RACE revealed that the SolWD40-repeat mRNA is cleaved at the predicted target site showing complementarity to a corresponding TPMVd-sRNA identified in silico. Our approach proved to be useful for the identification of natural host genes containing sequence homologies with segments of the Pospiviroidae genome. Using this strategy we identified a functionally conserved gene in Arabidopsis and tomato, whose expression was modified during viroid infection in the host genome; regulation of this gene expression could be guided by vd-sRNA:mRNA complementarity, suggesting that the comparison of the Arabidopsis genome to viroid sequences could lead to the identification of unexpected interactions between viroid RNAs and their host

  11. Genome-scale metabolic modeling and in silico analysis of lipid accumulating yeast Candida tropicalis for dicarboxylic acid production.

    PubMed

    Mishra, Pranjul; Park, Gyu-Yeon; Lakshmanan, Meiyappan; Lee, Hee-Seok; Lee, Hongweon; Chang, Matthew Wook; Ching, Chi Bun; Ahn, Jungoh; Lee, Dong-Yup

    2016-09-01

    Recently, the bio-production of α,ω-dicarboxylic acids (DCAs) has gained significant attention, which potentially leads to the replacement of the conventional petroleum-based products. In this regard, the lipid accumulating yeast Candida tropicalis, has been recognized as a promising microbial host for DCA biosynthesis: it possess the unique ω-oxidation pathway where the terminal carbon of α-fatty acids is oxidized to form DCAs with varying chain lengths. However, despite such industrial importance, its cellular physiology and lipid accumulation capability remain largely uncharacterized. Thus, it is imperative to better understand the metabolic behavior of this lipogenic yeast, which could be achieved by a systems biological approach. To this end, herein, we reconstructed the genome-scale metabolic model of C. tropicalis, iCT646, accounting for 646 unique genes, 945 metabolic reactions, and 712 metabolites. Initially, the comparative network analysis of iCT646 with other yeasts revealed several distinctive metabolic reactions, mainly within the amino acid and lipid metabolism including the ω-oxidation pathway. Constraints-based flux analysis was, then, employed to predict the in silico growth rates of C. tropicalis which are highly consistent with the cellular phenotype observed in glucose and xylose minimal media chemostat cultures. Subsequently, the lipid accumulation capability of C. tropicalis was explored in comparison with Saccharomyces cerevisiae, indicating that the formation of "citrate pyruvate cycle" is essential to the lipid accumulation in oleaginous yeasts. The in silico flux analysis also highlighted the enhanced ability of pentose phosphate pathway as NADPH source rather than malic enzyme during lipogenesis. Finally, iCT646 was successfully utilized to highlight the key directions of C. tropicalis strain design for the whole cell biotransformation application to produce long-chain DCAs from alkanes. Biotechnol. Bioeng. 2016;113: 1993-2004.

  12. Hamlet's Transformation.

    NASA Astrophysics Data System (ADS)

    Usher, P. D.

    1997-12-01

    William Shakespeare's Hamlet has much evidence to suggest that the Bard was aware of the cosmological models of his time, specifically the geocentric bounded Ptolemaic and Tychonic models, and the infinite Diggesian. Moreover, Shakespeare describes how the Ptolemaic model is to be transformed to the Diggesian. Hamlet's "transformation" is the reason that Claudius, who personifies the Ptolemaic model, summons Rosencrantz and Guildenstern, who personify the Tychonic. Pantometria, written by Leonard Digges and his son Thomas in 1571, contains the first technical use of the word "transformation." At age thirty, Thomas Digges went on to propose his Perfit Description, as alluded to in Act Five where Hamlet's age is given as thirty. In Act Five as well, the words "bore" and "arms" refer to Thomas' vocation as muster-master and his scientific interest in ballistics. England's leading astronomer was also the father of the poet whose encomium introduced the First Folio of 1623. His oldest child Dudley became a member of the Virginia Company and facilitated the writing of The Tempest. Taken as a whole, such manifold connections to Thomas Digges support Hotson's contention that Shakespeare knew the Digges family. Rosencrantz and Guildenstern in Hamlet bear Danish names because they personify the Danish model, while the king's name is latinized like that of Claudius Ptolemaeus. The reason Shakespeare anglicized "Amleth" to "Hamlet" was because he saw a parallel between Book Three of Saxo Grammaticus and the eventual triumph of the Diggesian model. But Shakespeare eschewed Book Four, creating this particular ending from an infinity of other possibilities because it "suited his purpose," viz. to celebrate the concept of a boundless universe of stars like the Sun.

  13. TRANSFORMER APPARATUS

    DOEpatents

    Wolfgang, F.; Nicol, J.

    1962-11-01

    Transformer apparatus is designed for measuring the amount of a paramagnetic substance dissolved or suspended in a diamagnetic liquid. The apparatus consists of a cluster of tubes, some of which are closed and have sealed within the diamagnetic substance without any of the paramagnetic material. The remaining tubes are open to flow of the mix- ture. Primary and secondary conductors are wrapped around the tubes in such a way as to cancel noise components and also to produce a differential signal on the secondaries based upon variations of the content of the paramagnetic material. (AEC)

  14. Rotary Transformer

    NASA Technical Reports Server (NTRS)

    McLyman, Colonel Wm. T.

    1996-01-01

    None given. From first Par: Many spacecraft (S/C) and surface rovers require the transfer of signals and power across rotating interfaces. Science instruments, antennas and solar arrays are elements needing rotary power transfer for certain (S/C) configurations. Delivery of signal and power has mainly been done by using the simplest means, the slip ring approach. This approach, although simple, leaves debris generating noise over a period of time...The rotary transformer is a good alternative to slip rings for signal and power transfer.

  15. Corn transformed

    SciTech Connect

    Moffat, A.S.

    1990-08-10

    Researchers have produced fertile corn transformed with a foreign gene that makes the plants resistant to the herbicide bialaphos. This achievement, is the first report of fertile transgenic corn in the reviewed literature, and it is the capstone of almost a decade's efforts to genetically engineer this country's most important crop. The only other major crop to be so manipulated is rice. The ability produce transgenic corn gives biologists a valuable tool to probe the whys and hows of gene expression and regulation. It may also give plant breeders a way to develop new corn varieties with a speed and predictability that would be impossible with classical breeding techniques.

  16. In silico prediction of drug therapy in catecholaminergic polymorphic ventricular tachycardia

    PubMed Central

    Yang, Pei‐Chi; Moreno, Jonathan D.; Miyake, Christina Y.; Vaughn‐Behrens, Steven B.; Jeng, Mao‐Tsuen; Grandi, Eleonora; Wehrens, Xander H. T.; Noskov, Sergei Y.

    2015-01-01

    Key points The mechanism of therapeutic efficacy of flecainide for catecholaminergic polymorphic ventricular tachycardia (CPVT) is unclear.Model predictions suggest that Na+ channel effects are insufficient to explain flecainide efficacy in CPVT.This study represents a first step toward predicting therapeutic mechanisms of drug efficacy in the setting of CPVT and then using these mechanisms to guide modelling and simulation to predict alternative drug therapies. Abstract Catecholaminergic polymorphic ventricular tachycardia (CPVT) is an inherited arrhythmia syndrome characterized by fatal ventricular arrhythmias in structurally normal hearts during β‐adrenergic stimulation. Current treatment strategies include β‐blockade, flecainide and ICD implementation – none of which is fully effective and each comes with associated risk. Recently, flecainide has gained considerable interest in CPVT treatment, but its mechanism of action for therapeutic efficacy is unclear. In this study, we performed in silico mutagenesis to construct a CPVT model and then used a computational modelling and simulation approach to make predictions of drug mechanisms and efficacy in the setting of CPVT. Experiments were carried out to validate model results. Our simulations revealed that Na+ channel effects are insufficient to explain flecainide efficacy in CPVT. The pure Na+ channel blocker lidocaine and the antianginal ranolazine were additionally tested and also found to be ineffective. When we tested lower dose combination therapy with flecainide, β‐blockade and CaMKII inhibition, our model predicted superior therapeutic efficacy than with flecainide monotherapy. Simulations indicate a polytherapeutic approach may mitigate side‐effects and proarrhythmic potential plaguing CPVT pharmacological management today. Importantly, our prediction of a novel polytherapy for CPVT was confirmed experimentally. Our simulations suggest that flecainide therapeutic efficacy in CPVT is unlikely

  17. Structural Investigation for Optimization of Anthranilic Acid Derivatives as Partial FXR Agonists by in Silico Approaches.

    PubMed

    Chen, Meimei; Yang, Xuemei; Lai, Xinmei; Kang, Jie; Gan, Huijuan; Gao, Yuxing

    2016-01-01

    In this paper, a three level in silico approach was applied to investigate some important structural and physicochemical aspects of a series of anthranilic acid derivatives (AAD) newly identified as potent partial farnesoid X receptor (FXR) agonists. Initially, both two and three-dimensional quantitative structure activity relationship (2D- and 3D-QSAR) studies were performed based on such AAD by a stepwise technology combined with multiple linear regression and comparative molecular field analysis. The obtained 2D-QSAR model gave a high predictive ability (R²train = 0.935, R²test = 0.902, Q²LOO = 0.899). It also uncovered that number of rotatable single bonds (b_rotN), relative negative partial charges (RPC(-)), oprea's lead-like (opr_leadlike), subdivided van der Waal's surface area (SlogP_VSA2) and accessible surface area (ASA) were important features in defining activity. Additionally, the derived3D-QSAR model presented a higher predictive ability (R²train = 0.944, R²test = 0.892, Q²LOO = 0.802). Meanwhile, the derived contour maps from the 3D-QSAR model revealed the significant structural features (steric and electronic effects) required for improving FXR agonist activity. Finally, nine newly designed AAD with higher predicted EC50 values than the known template compound were docked into the FXR active site. The excellent molecular binding patterns of these molecules also suggested that they can be robust and potent partial FXR agonists in agreement with the QSAR results. Overall, these derived models may help to identify and design novel AAD with better FXR agonist activity. PMID:27070594

  18. In silico studies of the interaction between BRN2 protein and MORE DNA.

    PubMed

    do Vale Coelho, Ivan Evangelista; Arruda, Denise Costa; Taranto, Alex Gutterres

    2016-09-01

    The incidence of skin cancer has increased in recent decades, and melanoma is the most aggressive form with the lowest chance of successful treatment. Currently, drug design projects are in progress, but available treatments against metastatic melanoma have not significantly increased survival, and few patients are cured. Thus, new therapeutic agents should be developed as more effective therapeutic options for melanoma. High levels of the BRN2 transcription factor have been related to melanoma development. However, neither the three-dimensional (3D) structure of BRN2 protein nor its POU domain has been determined experimentally. Construction of the BRN2 3D structure, and the study of its interaction with its DNA target, are important strategies for increasing the structural and functional knowledge of this protein. Thus, the aim of this work was to study the interaction between BRN2 and MORE DNA through in silico methods. The full-length BRN2 3D structure was built using the PHYRE2 and Swiss-Model programs, and molecular dynamics of this protein in complex with MORE DNA was simulated for 20 ns by the NAMD program. The BRN2 model obtained includes helix and loop regions, and the BRN2 POU domain shares structural similarity with other members of the transcription factor family. No significant conformational change of this protein occurred during dynamics simulation. These analyses revealed BRN2 residues important for the specific interaction with nucleotide bases and with more than one DNA nucleotide. This study may contribute to the design of inhibitors against BRN2 or MORE DNA as molecular targets of melanoma skin cancer. Graphical Abstract Model of complete Brn2 protein in complex with MORE DNA after building through comparative modeling and refinement by molecular dynamics simulation. PMID:27568376

  19. Structural Investigation for Optimization of Anthranilic Acid Derivatives as Partial FXR Agonists by in Silico Approaches

    PubMed Central

    Chen, Meimei; Yang, Xuemei; Lai, Xinmei; Kang, Jie; Gan, Huijuan; Gao, Yuxing

    2016-01-01

    In this paper, a three level in silico approach was applied to investigate some important structural and physicochemical aspects of a series of anthranilic acid derivatives (AAD) newly identified as potent partial farnesoid X receptor (FXR) agonists. Initially, both two and three-dimensional quantitative structure activity relationship (2D- and 3D-QSAR) studies were performed based on such AAD by a stepwise technology combined with multiple linear regression and comparative molecular field analysis. The obtained 2D-QSAR model gave a high predictive ability (R2train = 0.935, R2test = 0.902, Q2LOO = 0.899). It also uncovered that number of rotatable single bonds (b_rotN), relative negative partial charges (RPC−), oprea's lead-like (opr_leadlike), subdivided van der Waal’s surface area (SlogP_VSA2) and accessible surface area (ASA) were important features in defining activity. Additionally, the derived3D-QSAR model presented a higher predictive ability (R2train = 0.944, R2test = 0.892, Q2LOO = 0.802). Meanwhile, the derived contour maps from the 3D-QSAR model revealed the significant structural features (steric and electronic effects) required for improving FXR agonist activity. Finally, nine newly designed AAD with higher predicted EC50 values than the known template compound were docked into the FXR active site. The excellent molecular binding patterns of these molecules also suggested that they can be robust and potent partial FXR agonists in agreement with the QSAR results. Overall, these derived models may help to identify and design novel AAD with better FXR agonist activity. PMID:27070594

  20. An integrated molecular modeling approach for in silico design of new tetracyclic derivatives as ALK inhibitors.

    PubMed

    Peddi, Saikiran Reddy; Sivan, Sree Kanth; Manga, Vijjulatha

    2016-10-01

    Anaplastic lymphoma kinase (ALK), a promising therapeutic target for treatment of human cancers, is a receptor tyrosine kinase that instigates the activation of several signal transduction pathways. In the present study, in silico methods have been employed in order to explore the structural features and functionalities of a series of tetracyclic derivatives displaying potent inhibitory activity toward ALK. Initially docking was performed using GLIDE 5.6 to probe the bioactive conformation of all the compounds and to understand the binding modes of inhibitors. The docking results revealed that ligand interaction with Met 1199 plays a crucial role in binding of inhibitors to ALK. Further to establish a robust 3D-QSAR model using CoMFA and CoMSIA methods, the whole dataset was divided into three splits. Model obtained from Split 3 showed high accuracy ([Formula: see text] of 0.700 and 0.682, [Formula: see text] of 0.971 and 0.974, [Formula: see text] of 0.673 and 0.811, respectively for CoMFA and CoMSIA). The key structural requirements for enhancing the inhibitory activity were derived from CoMFA and CoMSIA contours in combination with site map analysis. Substituting small electronegative groups at Position 8 by replacing either morpholine or piperidine rings and maintaining hydrophobic character at Position 9 in tetracyclic derivatives can enhance the inhibitory potential. Finally, we performed molecular dynamics simulations in order to investigate the stability of protein ligand interactions and MM/GBSA calculations to compare binding free energies of co-crystal ligand and newly designed molecule N1. Based on the coherence of outcome of various molecular modeling studies, a set of 11 new molecules having potential predicted inhibitory activity were designed. PMID:26758803

  1. In silico investigation of pH-dependence of prolactin and human growth hormone binding to human prolactin receptor

    PubMed Central

    Wang, Lin; Witham, Shawn; Zhang, Zhe; Li, Lin; Hodsdon, Michael E.; Alexov, Emil

    2011-01-01

    Experimental data shows that the binding of human prolactin (hPRL) to human prolactin receptor (hPRLr-ECD) is strongly pH-dependent, while the binding of the same receptor to human growth hormone (hGH) is pH-independent. Here we carry in silico analysis of the molecular effects causing such a difference and reveal the role of individual amino acids. It is shown that the computational modeling correctly predicts experimentally determined pKa’s of histidine residues in an unbound state in the majority of the cases and the pH-dependence of the binding free energy. Structural analysis carried in conjunction with calculated pH-dependence of the binding revealed that the main reason for pH-dependence of the binding of hPRL-hPRLr-ECD is a number of salt- bridges across the interface of the complex, while no salt-bridges are formed in the hGH-hPRlr-ECD. Specifically, most of the salt-bridges involve histidine residues and this is the reason for the pH-dependence across a physiological range of pH. The analysis not only revealed the molecular mechanism of the pH-dependence of the hPRL-hPRLr-ECD, but also provided critical insight into the underlying physic-chemical mechanism. PMID:24683423

  2. Global Expression Profiling of Fibroblast Responses to Transforming Growth Factor-β1 Reveals the Induction of Inhibitor of Differentiation-1 and Provides Evidence of Smooth Muscle Cell Phenotypic Switching

    PubMed Central

    Chambers, Rachel C.; Leoni, Patricia; Kaminski, Naftali; Laurent, Geoffrey J.; Heller, Renu A.

    2003-01-01

    Transforming growth factor-β1 (TGF-β1) plays a central role in promoting extracellular matrix protein deposition by promoting the transformation of fibroblasts to myofibroblasts. To gain new insights into the transcriptional programs involved, we profiled human fetal lung fibroblast global gene expression in response to TGF-β1 up to 24 hours using oligonucleotide microarrays. In this report, we present data for 146 genes that were up-regulated at least twofold at two time points. These genes group into several major functional categories, including genes involved in cytoskeletal reorganization (n = 30), matrix formation (n = 25), metabolism and protein biosynthesis (n = 27), cell signaling (n = 21), proliferation and survival (n = 13), gene transcription (n = 9), and of uncertain function (n = 21). For 80 of these genes, this is the first report that they are TGF-β1-responsive. The early induction of two members of the inhibitor of differentiation (ID) family of transcriptional regulators, ID1 and ID3, was followed by the up-regulation of a number of genes that are usually expressed by highly differentiated smooth muscle cells, including smooth muscle myosin heavy chain, basic calponin, and smoothelin. These findings were confirmed at the protein level for primary adult lung fibroblasts. ID1 further behaved like a typical immediate-early gene and, unlike ID3, was expressed and induced at the protein level. Immunohistochemical analysis showed that ID1 was highly expressed by (myo)fibroblasts within fibrotic foci in experimentally induced pulmonary fibrosis. ID1 acts as a dominant-negative antagonist of basic helix-loop-helix transcription factors that drive cell lineage commitment and differentiation. These findings have important implications for our understanding of fibroblast transcriptional programming in response to TGF-β1 during development, oncogenesis, tissue repair, and fibrosis. PMID:12547711

  3. Comparison of different transformation methods for Aspergillus giganteus.

    PubMed

    Meyer, Vera; Mueller, Dirk; Strowig, Till; Stahl, Ulf

    2003-08-01

    Four different transformation methods were tested and compared in an attempt to facilitate the genetic transformation of Aspergillus giganteus, the producer of an antifungal protein (AFP). The fungus was transformed to hygromycin B resistance, using the hph gene of Escherichia coli by protoplast transformation, electroporation, biolistic transformation, and Agrobacterium tumefaciens-mediated transformation. Electroporation and biolistic transformation were found to be inappropriate for transforming A. giganteus, due to a low transformation yield. The conventional transformation technique based on protoplasts yielded up to 55 transformants in 10(8) protoplasts/microg DNA and was enhanced to 140-fold by A. tumefaciens-mediated transfer of its T-DNA. Here, the germination time prior to cocultivation and the fungus:bacterium ratio were found to alter the transformation efficiency. Southern blot analysis revealed that the A. giganteus transformants contained a randomly integrated single T-DNA copy, whereas multiple integration events were frequent in transformants obtained by the protoplast method. PMID:12756496

  4. In vitro and in silico toxicity evaluation of bioactive 4'-aminochalcone derivatives.

    PubMed

    Mariño, Patrícia Albano; Pereira, Danillo Baptista; Santi, Gustavo; de Souza, Raul Oliveira; Faoro, Débora; de Oliveira, Luís Flávio Souza; Machado, Michel Mansur; Paula, Fávero Reisdorfer

    2016-04-01

    The 4'-aminochalcones compounds are open-chain flavonoids structures which have shown a known array of pharmacological activities, such as antibacterial, antifungal, anti-inflammatory and antitumor effects. There is little toxicological information available about these compounds in the literature. Therefore, the investigation of toxic effects of three 4'-aminochalcone derivatives was performed using in silico and in vitro assays. In silico provided results that indicated the occurrence of mutagenic and genotoxic effects. In vitro tests, using Cellular Proliferation and Viability, Micronucleus, and DNA damage by Comet assay, showed that the compounds studied also present mutagenic and genotoxic effects, which confirm the result determined by the in silico analysis. The use of experimental and computational models is complementary to each other and the results determined for 4'-aminochalones suggest that the chalcones should also be carefully considered since they show some risks to cause toxic effects to human cells. PMID:26154124

  5. Transformational leadership.

    PubMed

    Marlow, D L

    1996-01-01

    In these uncertain times in the healthcare industry, administrators are asked to do more with less time and resources. Because of the extended roles they are playing in today's organizations, radiology administrators are looked upon as agents of change. What leadership skills do they need in this turbulent and uncertain healthcare environment? What are the trait's of tomorrow's leaders? The transformational leader is the one who will guide us through this changing healthcare environment. Several behavioral patterns emerge as important traits for tomorrow's leaders to have-individual consideration, intellectual stimulation and charisma. Tomorrow's leader must view each person as an individual, showing genuine concern and belief in each person's ability to perform. Transformational leaders stimulate others by encouraging them to be curious and try new ideas. The final characteristic, charisma, is the ability to inspire others. Luckily, leaders are made, not born: today's leaders can learn to be responsive, to draw out new ideas from employees, and to communicate self-esteem, energy and enthusiasm. PMID:10163135

  6. In silico modeling predicts drug sensitivity of patient-derived cancer cells

    PubMed Central

    2014-01-01

    Background Glioblastoma (GBM) is an aggressive disease associated with poor survival. It is essential to account for the complexity of GBM biology to improve diagnostic and therapeutic strategies. This complexity is best represented by the increasing amounts of profiling (“omics”) data available due to advances in biotechnology. The challenge of integrating these vast genomic and proteomic data can be addressed by a comprehensive systems modeling approach. Methods Here, we present an in silico model, where we simulate GBM tumor cells using genomic profiling data. We use this in silico tumor model to predict responses of cancer cells to targeted drugs. Initially, we probed the results from a recent hypothesis-independent, empirical study by Garnett and co-workers that analyzed the sensitivity of hundreds of profiled cancer cell lines to 130 different anticancer agents. We then used the tumor model to predict sensitivity of patient-derived GBM cell lines to different targeted therapeutic agents. Results Among the drug-mutation associations reported in the Garnett study, our in silico model accurately predicted ~85% of the associations. While testing the model in a prospective manner using simulations of patient-derived GBM cell lines, we compared our simulation predictions with experimental data using the same cells in vitro. This analysis yielded a ~75% agreement of in silico drug sensitivity with in vitro experimental findings. Conclusions These results demonstrate a strong predictability of our simulation approach using the in silico tumor model presented here. Our ultimate goal is to use this model to stratify patients for clinical trials. By accurately predicting responses of cancer cells to targeted agents a priori, this in silico tumor model provides an innovative approach to personalizing therapy and promises to improve clinical management of cancer. PMID:24884660

  7. The acceptance of in silico models for REACH: Requirements, barriers, and perspectives

    PubMed Central

    2011-01-01

    In silico models have prompted considerable interest and debate because of their potential value in predicting the properties of chemical substances for regulatory purposes. The European REACH legislation promotes innovation and encourages the use of alternative methods, but in practice the use of in silico models is still very limited. There are many stakeholders influencing the regulatory trajectory of quantitative structure-activity relationships (QSAR) models, including regulators, industry, model developers and consultants. Here we outline some of the issues and challenges involved in the acceptance of these methods for regulatory purposes. PMID:21982269

  8. In silico allergenicity prediction of several lipid transfer proteins.

    PubMed

    Garino, Cristiano; Coïsson, Jean Daniel; Arlorio, Marco

    2016-02-01

    Non-specific lipid transfer proteins (nsLTPs) are common allergens and they are particularly widespread within the plant kingdom. They have a highly conserved three-dimensional structure that generate a strong cross-reactivity among the members of this family. In the last years several web tools for the prediction of allergenicity of new molecules based on their homology with known allergens have been released, and guidelines to assess potential allergenicity of proteins through bioinformatics have been established. Even if such tools are only partially reliable yet, they can provide important indications when other kinds of molecular characterization are lacking. The potential allergenicity of 28 amino acid sequences of LTPs homologs, either retrieved from the UniProt database or in silico deduced from the corresponding EST coding sequence, was predicted using 7 publicly available web tools. Moreover, their similarity degree to their closest known LTP allergens was calculated, in order to evaluate their potential cross-reactivity. Finally, all sequences were studied for their identity degree with the peach allergen Pru p 3, considering the regions involved in the formation of its known conformational IgE-binding epitope. Most of the analyzed sequences displayed a high probability to be allergenic according to all the software employed. The analyzed LTPs from bell pepper, cassava, mango, mungbean and soybean showed high homology (>70%) with some known allergenic LTPs, suggesting a potential risk of cross-reactivity for sensitized individuals. Other LTPs, like for example those from canola, cassava, mango, mungbean, papaya or persimmon, displayed a high degree of identity with Pru p 3 within the consensus sequence responsible for the formation, at three-dimensional level, of its major conformational epitope. Since recent studies highlighted how in patients mono-sensitized to peach LTP the levels of IgE seem directly proportional to the chance of developing cross

  9. Herbicide Transformation

    PubMed Central

    Lanzilotta, R. P.; Pramer, David

    1970-01-01

    A strain of Fusarium solani isolated from soil by enrichment techniques used propanil (3′, 4′-dichloropropionanilide) as a sole source of organic carbon and energy for growth in pure culture. The primary product of the transformation of propanil by F. solani was isolated and identified as 3,4-dichloroaniline (DCA). This compound accumulated in the medium to a level (80 μg/ml) which stopped further herbicide utilization. Herbicide utilization by F. solani was influenced by various environmental and nutritional factors. It was more sensitive to acid than alkaline pH. Added glucose and yeast extract increased the rate of propanil decomposition, and the reduced aeration retarded growth of the fungus and herbicide utilization. The growth of F. solani on propionate was inhibited by added DCA. Images PMID:5437305

  10. Identifying potential endocrine disruptors among industrial chemicals and their metabolites--development and evaluation of in silico tools.

    PubMed

    Rybacka, Aleksandra; Rudén, Christina; Tetko, Igor V; Andersson, Patrik L

    2015-11-01

    The aim of this study was to improve the identification of endocrine disrupting chemicals (EDCs) by developing and evaluating in silico tools that predict interactions at the estrogen (E) and androgen (A) receptors, and binding to transthyretin (T). In particular, the study focuses on evaluating the use of the EAT models in combination with a metabolism simulator to study the significance of bioactivation for endocrine disruption. Balanced accuracies of the EAT models ranged from 77-87%, 62-77%, and 65-89% for E-, A-, and T-binding respectively. The developed models were applied on a set of more than 6000 commonly used industrial chemicals of which 9% were predicted E- and/or A-binders and 1% were predicted T-binders. The numbers of E- and T-binders increased 2- and 3-fold, respectively, after metabolic transformation, while the number of A-binders marginally changed. In-depth validation confirmed that several of the predicted bioactivated E- or T-binders demonstrated in vivo estrogenic activity or influenced blood levels of thyroxine in vivo. The metabolite simulator was evaluated using in vivo data from the literature which showed a 50% accuracy for studied chemicals. The study stresses, in summary, the importance of including metabolic activation in prioritization activities of potentially emerging contaminants. PMID:26210185

  11. Revealing Rembrandt

    PubMed Central

    Parker, Andrew J.

    2014-01-01

    The power and significance of artwork in shaping human cognition is self-evident. The starting point for our empirical investigations is the view that the task of neuroscience is to integrate itself with other forms of knowledge, rather than to seek to supplant them. In our recent work, we examined a particular aspect of the appreciation of artwork using present-day functional magnetic resonance imaging (fMRI). Our results emphasized the continuity between viewing artwork and other human cognitive activities. We also showed that appreciation of a particular aspect of artwork, namely authenticity, depends upon the co-ordinated activity between the brain regions involved in multiple decision making and those responsible for processing visual information. The findings about brain function probably have no specific consequences for understanding how people respond to the art of Rembrandt in comparison with their response to other artworks. However, the use of images of Rembrandt's portraits, his most intimate and personal works, clearly had a significant impact upon our viewers, even though they have been spatially confined to the interior of an MRI scanner at the time of viewing. Neuroscientific studies of humans viewing artwork have the capacity to reveal the diversity of human cognitive responses that may be induced by external advice or context as people view artwork in a variety of frameworks and settings. PMID:24795552

  12. In silico identification and comparative genomics of candidate genes involved in biosynthesis and accumulation of seed oil in plants.

    PubMed

    Sharma, Arti; Chauhan, Rajinder Singh

    2012-01-01

    Genes involved in fatty acids biosynthesis, modification and oil body formation are expected to be conserved in structure and function in different plant species. However, significant differences in the composition of fatty acids and total oil contents in seeds have been observed in different plant species. Comparative genomics was performed on 261 genes involved in fatty acids biosynthesis, TAG synthesis, and oil bodies formation in Arabidopsis, Brassica rapa, castor bean and soybean. In silico expression analysis revealed that stearoyl desaturase, FatB, FAD2, oleosin and DGAT are highly abundant in seeds, thereby considered as ideal candidates for mining of favorable alleles in natural population. Gene structure analysis for major genes, ACCase, FatA, FatB, FAD2, FAD3 and DGAT, which are known to play crucial role in oil synthesis revealed that there are uncommon variations (SNPs and INDELs) which lead to varying content and composition of fatty acids in seed oil. The predicted variations can provide good targets for seed oil QTL identification, understanding the molecular mechanism of seed oil accumulation, and genetic modification to enhance seed oil yield in plants. PMID:22312320

  13. Inhibition of cytochrome P450 3A by acetoxylated analogues of resveratrol in in vitro and in silico models

    PubMed Central

    Basheer, Loai; Schultz, Keren; Kerem, Zohar

    2016-01-01

    Many dietary compounds, including resveratrol, are potent inhibitors of CYP3A4. Here we examined the potential to predict inhibition capacity of dietary polyphenolics using an in silico and in vitro approaches and synthetic model compounds. Mono, di, and tri-acetoxy resveratrol were synthesized, a cell line of human intestine origin and microsomes from rat liver served to determine their in vitro inhibition of CYP3A4, and compared to that of resveratrol. Docking simulation served to predict the affinity of the synthetic model compounds to the enzyme. Modelling of the enzyme’s binding site revealed three types of interaction: hydrophobic, electrostatic and H-bonding. The simulation revealed that each of the examined acetylations of resveratrol led to the loss of important interactions of all types. Tri-acetoxy resveratrol was the weakest inhibitor in vitro despite being the more lipophilic and having the highest affinity for the binding site. The simulation demonstrated exclusion of all interactions between tri-acetoxy resveratrol and the heme due to distal binding, highlighting the complexity of the CYP3A4 binding site, which may allow simultaneous accommodation of two molecules. Finally, the use of computational modelling may serve as a quick predictive tool to identify potential harmful interactions between dietary compounds and prescribed drugs. PMID:27530542

  14. Inhibition of cytochrome P450 3A by acetoxylated analogues of resveratrol in in vitro and in silico models.

    PubMed

    Basheer, Loai; Schultz, Keren; Kerem, Zohar

    2016-01-01

    Many dietary compounds, including resveratrol, are potent inhibitors of CYP3A4. Here we examined the potential to predict inhibition capacity of dietary polyphenolics using an in silico and in vitro approaches and synthetic model compounds. Mono, di, and tri-acetoxy resveratrol were synthesized, a cell line of human intestine origin and microsomes from rat liver served to determine their in vitro inhibition of CYP3A4, and compared to that of resveratrol. Docking simulation served to predict the affinity of the synthetic model compounds to the enzyme. Modelling of the enzyme's binding site revealed three types of interaction: hydrophobic, electrostatic and H-bonding. The simulation revealed that each of the examined acetylations of resveratrol led to the loss of important interactions of all types. Tri-acetoxy resveratrol was the weakest inhibitor in vitro despite being the more lipophilic and having the highest affinity for the binding site. The simulation demonstrated exclusion of all interactions between tri-acetoxy resveratrol and the heme due to distal binding, highlighting the complexity of the CYP3A4 binding site, which may allow simultaneous accommodation of two molecules. Finally, the use of computational modelling may serve as a quick predictive tool to identify potential harmful interactions between dietary compounds and prescribed drugs. PMID:27530542

  15. In Silico Identification and Comparative Genomics of Candidate Genes Involved in Biosynthesis and Accumulation of Seed Oil in Plants

    PubMed Central

    Sharma, Arti; Chauhan, Rajinder Singh

    2012-01-01

    Genes involved in fatty acids biosynthesis, modification and oil body formation are expected to be conserved in structure and function in different plant species. However, significant differences in the composition of fatty acids and total oil contents in seeds have been observed in different plant species. Comparative genomics was performed on 261 genes involved in fatty acids biosynthesis, TAG synthesis, and oil bodies formation in Arabidopsis, Brassica rapa, castor bean and soybean. In silico expression analysis revealed that stearoyl desaturase, FatB, FAD2, oleosin and DGAT are highly abundant in seeds, thereby considered as ideal candidates for mining of favorable alleles in natural population. Gene structure analysis for major genes, ACCase, FatA, FatB, FAD2, FAD3 and DGAT, which are known to play crucial role in oil synthesis revealed that there are uncommon variations (SNPs and INDELs) which lead to varying content and composition of fatty acids in seed oil. The predicted variations can provide good targets for seed oil QTL identification, understanding the molecular mechanism of seed oil accumulation, and genetic modification to enhance seed oil yield in plants. PMID:22312320

  16. In silico mechanistic analysis of IRF3 inactivation and high-risk HPV E6 species-dependent drug response

    PubMed Central

    Shah, Masaud; Anwar, Muhammad Ayaz; Park, Seolhee; Jafri, Syyada Samra; Choi, Sangdun

    2015-01-01

    The high-risk human papillomavirus E6 (hrHPV E6) protein has been widely studied due to its implication in cervical cancer. In response to viral threat, activated kinases phosphorylate the IRF3 autoinhibitory domain, inducing type1 interferon production. HPV circumvents the antiviral response through the possible E6 interaction with IRF3 and abrogates p53’s apoptotic activity by recruiting E6-associated protein. However, the molecular mechanism of IRF3 inactivation by hrHPV E6 has not yet been delineated. Therefore, we explored this mechanism through in silico examination of protein-protein and protein-ligand docking, binding energy differences, and computational alanine mutagenesis. Our results suggested that the LxxLL motifs of IRF3 binds within the hydrophobic pocket of E6, precluding Ser-patch phosphorylation, necessary for IRF3 activation and interferon induction. This model was further supported by molecular dynamics simulation. Furthermore, protein-ligand docking and drug resistance modeling revealed that the polar patches in the pocket of E6, which are crucial for complex stability and ligand binding, are inconsistent among hrHPV species. Such variabilities pose a risk of treatment failure owing to point mutations that might render drugs ineffective, and allude to multi-drug therapy. Overall, this study reveals a novel perspective of innate immune suppression in HPV infections and suggests a plausible therapeutic intervention. PMID:26289783

  17. In silico mechanistic analysis of IRF3 inactivation and high-risk HPV E6 species-dependent drug response.

    PubMed

    Shah, Masaud; Anwar, Muhammad Ayaz; Park, Seolhee; Jafri, Syyada Samra; Choi, Sangdun

    2015-01-01

    The high-risk human papillomavirus E6 (hrHPV E6) protein has been widely studied due to its implication in cervical cancer. In response to viral threat, activated kinases phosphorylate the IRF3 autoinhibitory domain, inducing type1 interferon production. HPV circumvents the antiviral response through the possible E6 interaction with IRF3 and abrogates p53's apoptotic activity by recruiting E6-associated protein. However, the molecular mechanism of IRF3 inactivation by hrHPV E6 has not yet been delineated. Therefore, we explored this mechanism through in silico examination of protein-protein and protein-ligand docking, binding energy differences, and computational alanine mutagenesis. Our results suggested that the LxxLL motifs of IRF3 binds within the hydrophobic pocket of E6, precluding Ser-patch phosphorylation, necessary for IRF3 activation and interferon induction. This model was further supported by molecular dynamics simulation. Furthermore, protein-ligand docking and drug resistance modeling revealed that the polar patches in the pocket of E6, which are crucial for complex stability and ligand binding, are inconsistent among hrHPV species. Such variabilities pose a risk of treatment failure owing to point mutations that might render drugs ineffective, and allude to multi-drug therapy. Overall, this study reveals a novel perspective of innate immune suppression in HPV infections and suggests a plausible therapeutic intervention. PMID:26289783

  18. Revealing Mercury

    NASA Astrophysics Data System (ADS)

    Prockter, L. M.; Solomon, S. C.; Head, J. W.; Watters, T. R.; Murchie, S. L.; Robinson, M. S.; Chapman, C. R.; McNutt, R. L.

    2009-04-01

    The MErcury Surface, Space ENvironment, GEochemistry, and Ranging (MESSENGER) spacecraft, developed under NASA's Discovery Program, launched in August 2004. En route to insertion into orbit about Mercury in 2011, MESSENGER flies by Mercury three times. The first and second of these encounters were accomplished in January and October of 2008. These flybys viewed portions of Mercury's surface that were not observed by Mariner 10 during its reconnaissance of somewhat less than half of the planet in 1974-1975. All MESSENGER instruments operated during each flyby and returned a wealth of new data. Many of the new observations were focused on the planet's geology, including monochrome imaging at resolutions as high as 100 m/pixel, multispectral imaging in 11 filters at resolutions as high as 500 m/pixel, laser altimetry tracks extending over several thousands of kilometers, and high-resolution spectral measurements of several types of terrain. Here we present an overview of the first inferences on the global geology of Mercury from the MESSENGER observations. Whereas evidence for volcanism was equivocal from Mariner 10 data, the new MESSENGER images and altimetry provide compelling evidence that volcanism was widespread and protracted on Mercury. Color imaging reveals three common spectral units on the surface: a higher-reflectance, relatively red material occurring as a distinct class of smooth plains, typically with distinct embayment relationships interpreted to indicate volcanic emplacement; a lower-reflectance, relatively blue material typically excavated by impact craters and therefore inferred to be more common at depth; and a spectrally intermediate terrain that constitutes much of the uppermost crust. Three more minor spectral units are also seen: fresh crater ejecta, reddish material associated with rimless depressions interpreted to be volcanic centers, and high-reflectance deposits seen in some crater floors. Preliminary measurements of crater size

  19. IN SILICO APPROACHES TO MECHANISTIC AND PREDICTIVE TOXICOLOGY: AN INTRODUCTION TO BIOINFORMATICS FOR TOXICOLOGISTS. (R827402)

    EPA Science Inventory

    Abstract

    Bioinformatics, or in silico biology, is a rapidly growing field that encompasses the theory and application of computational approaches to model, predict, and explain biological function at the molecular level. This information rich field requires new ...

  20. From FASTQ to Function: In Silico Methods for Processing Next-Generation Sequencing Data.

    PubMed

    Preston, Mark D; Stabler, Richard A

    2016-01-01

    This chapter presents a method to process C. difficile whole-genome next-generation sequencing data straight from the sequencer. Quality control processing and de novo assembly of these data enable downstream analyses such as gene annotation and in silico multi-locus strain-type identification. PMID:27507331

  1. In silico risk assessment for skin sensitization using artificial neural network analysis.

    PubMed

    Tsujita-Inoue, Kyoko; Atobe, Tomomi; Hirota, Morihiko; Ashikaga, Takao; Kouzuki, Hirokazu

    2015-04-01

    The sensitizing potential of chemicals is usually identified and characterized using in vivo methods such as the murine local lymph node assay (LLNA). Due to regulatory constraints and ethical concerns, alternatives to animal testing are needed to predict the skin sensitization potential of chemicals. For this purpose, an integrated evaluation system employing multiple in vitro and in silico parameters that reflect different aspects of the sensitization process seems promising. We previously reported that LLNA thresholds could be well predicted by using an artificial neural network (ANN) model, designated iSENS ver. 2 (integrating in vitro sensitization tests version 2), to analyze data obtained from in vitro tests focused on different aspects of skin sensitization. Here, we examined whether LLNA thresholds could be predicted by ANN using in silico-calculated descriptors of the three-dimensional structures of chemicals. We obtained a good correlation between predicted LLNA thresholds and reported values. Furthermore, combining the results of the in vitro (iSENS ver. 2) and in silico models reduced the number of chemicals for which the potency category was under-estimated. In conclusion, the ANN model using in silico parameters was shown to be have useful predictive performance. Further, our results indicate that the combination of this model with a predictive model using in vitro data represents a promising approach for integrated risk assessment of skin sensitization potential of chemicals. PMID:25786524

  2. IN SILICO METHODOLOGIES FOR PREDICTIVE EVALUATION OF TOXICITY BASED ON INTEGRATION OF DATABASES

    EPA Science Inventory

    In silico methodologies for predictive evaluation of toxicity based on integration of databases

    Chihae Yang1 and Ann M. Richard2, 1LeadScope, Inc. 1245 Kinnear Rd. Columbus, OH. 43212 2National Health & Environmental Effects Research Lab, U.S. EPA, Research Triangle Park, ...

  3. In silico analysis of 454 data yields the complete American cranberry (Vaccinium macrocarpon Ait.) plastid genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The complete plastid genome sequence of the cranberry cultivar “HyRed” was reconstructed using next generation sequencing (NGS) data by in silico procedures. We used previously generated “HyRed” 454 shotgun sequence data to isolate plastid data via homology comparisons with complete sequences from s...

  4. TARGETED DELIVERY OF INHALED PHARMACEUTICALS USING AN IN SILICO DOSIMETRY MODEL

    EPA Science Inventory

    We present an in silico dosimetry model which can be used for inhalation toxicology (risk assessment of inhaled air pollutants) and aerosol therapy ( targeted delivery of inhaled drugs). This work presents scientific and clinical advances beyond the development of the original in...

  5. Searching the Sequence Space for Potent Aptamers Using SELEX in Silico.

    PubMed

    Zhou, Qingtong; Xia, Xiaole; Luo, Zhaofeng; Liang, Haojun; Shakhnovich, Eugene

    2015-12-01

    To isolate functional nucleic acids that bind to defined targets with high affinity and specificity, which are known as aptamers, the systematic evolution of ligands by exponential enrichment (SELEX) methodology has emerged as the preferred approach. Here, we propose a computational approach, SELEX in silico, that allows the sequence space to be more thoroughly explored regarding binding of a certain target. Our approach consists of two steps: (i) secondary structure-based sequence screening, which aims to collect the sequences that can form a desired RNA motif as an enhanced initial library, followed by (ii) sequence enrichment regarding target binding by molecular dynamics simulation-based virtual screening. Our SELEX in silico method provided a practical computational solution to three key problems in aptamer sequence searching: design of nucleic acid libraries, knowledge of sequence enrichment, and identification of potent aptamers. Six potent theophylline-binding aptamers, which were isolated by SELEX in silico from a sequence space containing 4(13) sequences, were experimentally verified to bind theophylline with high affinity: Kd ranging from 0.16 to 0.52 μM, compared with the dissociation constant of the original aptamer-theophylline, 0.32 μM. These results demonstrate the significant potential of SELEX in silico as a new method for aptamer discovery and optimization. PMID:26642994

  6. AN IN SILICO INVESTIGATION OF THE ENANTIOSELECTIVE METABOLISM RATES OF TRIAZOLE FUGICIDES

    EPA Science Inventory

    The objective of this work is to use in silico methods such as ab initio quantum and classical force-field methods to explore and develop an understanding for the enantioselective metabolism rates experimentally observed in the triazole fungicide bromuconazole. This directed stud...

  7. VIRTUAL LIVER: AN IN SILICO FRAMEWORK FOR ANALYZING CHEMICAL-INDUCED HEPATOTOXICITY

    EPA Science Inventory

    The US EPA Virtual Liver (v-LiverTM) is an in silico framework for the dose-dependent perturbation of normal hepatic functions by chemicals using in vitro data. The framework consists of a computable knowledge-base (KB) to infer putative pathways in hepatotoxicity and a cellular...

  8. Predicting myelosuppression of drugs from in silico models.

    PubMed

    Crivori, Patrizia; Pennella, Giulia; Magistrelli, Miriam; Grossi, Pietro; Giusti, Anna Maria

    2011-02-28

    Anticancer agents targeting proliferating cell populations in tumor as well as in normal tissues can lead to a number of side effects including hematotoxicity, a common dose-limiting toxicity associated with oncology drugs. Myelosuppression, regarded as unacceptable for other therapeutic indications, is considered a clinical risk also for new targeted anticancer drugs acting specifically on tumor cells. Thus, it becomes important not only to evaluate the potential toxicity of such new therapeutics to human hematopoietic tissue during preclinical development but also to anticipate this liability in early drug discovery. This could be achieved by using in silico models to guide the design of new lead compounds and the selection of analogs with reduced myelosuppressive potential. Hence, the purpose of this study was to develop computational models able to predict the potential myelotoxicity of drugs from their chemical structure. The data set analyzed included 38 drugs. The structural diversity and the drug-like space covered by these molecules were investigated using the ChemGPS methodology. Two sets of potentially relevant descriptors for modeling myelotoxicity (i.e., 3D Volsurf+ and 2D structural and electrotopological E-states descriptors) were selected and a Principal Component Analysis was carried out on the entire set of data. The first two PCs were able to discriminate the highest from the least myelotoxic compounds with a total accuracy of 95%. Then, a quantitative PLS model was developed by correlating a selected subset of in vitro hematotoxicity data with Volsurf+ descriptors. After variable selection, the PLS analysis resulted in a one-latent-variable model with r(2) of 0.79 and q(2) of 0.72. The inclusion of 2D descriptors in the PLS analysis improved only slightly the robustness and quality of the model that predicted the pIC(50) values of 21 drugs not included in the model with a RMSEP of 0.67 and a squared correlation coefficient (r(0)(2)) of 0

  9. In-silico analysis and expression profiling implicate diverse role of EPSPS family genes in regulating developmental and metabolic processes

    PubMed Central

    2014-01-01

    Background The EPSPS, EC 2.5.1.19 (5-enolpyruvylshikimate −3-phosphate synthase) is considered as one of the crucial enzyme in the shikimate pathway for the biosynthesis of essential aromatic amino acids and secondary metabolites in plants, fungi along with microorganisms. It is also proved as a specific target of broad spectrum herbicide glyphosate. Results On the basis of structure analysis, this EPSPS gene family comprises the presence of EPSPS I domain, which is highly conserved among different plant species. Here, we followed an in-silico approach to identify and characterize the EPSPS genes from different plant species. On the basis of their phylogeny and sequence conservation, we divided them in to two groups. Moreover, the interacting partners and co-expression data of the gene revealed the importance of this gene family in maintaining cellular and metabolic functions in the cell. The present study also highlighted the highest accumulation of EPSPS transcript in mature leaves followed by young leaves, shoot and roots of tobacco. In order to gain the more knowledge about gene family, we searched for the previously reported motifs and studied its structural importance on the basis of homology modelling. Conclusions The results presented here is a first detailed in-silico study to explore the role of EPSPS gene in forefront of different plant species. The results revealed a great deal for the diversification and conservation of EPSPS gene family across different plant species. Moreover, some of the EPSPS from different plant species may have a common evolutionary origin and may contain same conserved motifs with related and important molecular function. Most importantly, overall analysis of EPSPS gene elucidated its pivotal role in immense function within the plant, both in regulating plant growth as well its development throughout the life cycle of plant. Since EPSPS is a direct target of herbicide glyphosate, understanding its mechanism for regulating

  10. Integration of in silico modeling, prediction by binding energy and experimental approach to study the amorphous chitin nanocarriers for cancer drug delivery.

    PubMed

    Geetha, P; Sivaram, Amal J; Jayakumar, R; Gopi Mohan, C

    2016-05-20

    In silico modeling of the polymer-drug nanocarriers have now days became a powerful virtual screening tool for the optimization of new drug delivery systems. The interactions between amorphous chitin nanoparticles (AC-NPs) with three different types of anti-cancer drugs such as curcumin, docetaxel and 5-flurouracil were studied by integration of computational and experimental techniques. The drug entrapment and drug loading efficiency of these three drugs with AC-NPs were (98±1%), (77±2%), and (47±12%), respectively. Further, cytotoxicity and cellular uptake studies of drug loaded AC-NPs on Gastric adenocarcinoma (AGS) cells showed enhanced drug uptake and cancer cell death. In silico binding energy (BE) between AC-NPs with these anti-cancer drugs were studied by molecular docking technique. Computational drug's BEs are in excellent agreement with experimental AC-NPs drug loading (R(2)=0.9323) and drug entrapment (R(2)=0.9741) efficiencies. Thus, present integrated study revealed significant insight on chemical nature, strength, and putative interacting sites of anti-cancer drugs with AC-NPs. PMID:26917396

  11. Using in vitro/in silico data for consumer safety assessment of feed flavoring additives--A feasibility study using piperine.

    PubMed

    Thiel, A; Etheve, S; Fabian, E; Leeman, W R; Plautz, J R

    2015-10-01

    Consumer health risk assessment for feed additives is based on the estimated human exposure to the additive that may occur in livestock edible tissues compared to its hazard. We present an approach using alternative methods for consumer health risk assessment. The aim was to use the fewest possible number of animals to estimate its hazard and human exposure without jeopardizing the safety upon use. As an example we selected the feed flavoring substance piperine and applied in silico modeling for residue estimation, results from literature surveys, and Read-Across to assess metabolism in different species. Results were compared to experimental in vitro metabolism data in rat and chicken, and to quantitative analysis of residues' levels from the in vivo situation in livestock. In silico residue modeling showed to be a worst case: the modeled residual levels were considerably higher than the measured residual levels. The in vitro evaluation of livestock versus rodent metabolism revealed no major differences in metabolism between the species. We successfully performed a consumer health risk assessment without performing additional animal experiments. As shown, the use and combination of different alternative methods supports animal welfare consideration and provides future perspective to reducing the number of animals. PMID:26107290

  12. Detection of cis- and trans-acting Factors in DNA Structure-Induced Genetic Instability Using In silico and Cellular Approaches

    PubMed Central

    Wang, Guliang; Zhao, Junhua; Vasquez, Karen M.

    2016-01-01

    Sequences that can adopt alternative DNA structures (i.e., non-B DNA) are very abundant in mammalian genomes, and recent studies have revealed many important biological functions of non-B DNA structures in chromatin remodeling, DNA replication, transcription, and genetic instability. Here, we provide results from an in silico web-based search engine coupled with cell-based experiments to characterize the roles of non-B DNA conformations in genetic instability in eukaryotes. The purpose of this article is to illustrate strategies that can be used to identify and interrogate the biological roles of non-B DNA structures, particularly on genetic instability. We have included unpublished data using a short H-DNA-forming sequence from the human c-MYC promoter region as an example, and identified two different mechanisms of H-DNA-induced genetic instability in yeast and mammalian cells: a DNA replication-related model of mutagenesis; and a replication-independent cleavage model. Further, we identified candidate proteins involved in H-DNA-induced genetic instability by using a yeast genetic screen. A combination of in silico and cellular methods, as described here, should provide further insight into the contributions of non-B DNA structures in biological functions, genetic evolution, and disease development. PMID:27532010

  13. Repositioning of 2,4-dichlorophenoxy acetic acid as a potential anti-inflammatory agent: in silico and pharmaceutical formulation study.

    PubMed

    Khedr, Mohammed A; Shehata, Tamer M; Mohamed, Maged E

    2014-12-18

    2,4-Dichlorophenoxy acetic acid (2,4-D) is a well-known plant auxin which is widely used in plant tissue culture experiments as well as a weed killer and a herbicide. In this study, 2,4-D was rediscovered as a new anti-inflammatory agent through an in silico molecular modeling and docking studies along with drug formulation and in vivo anti-inflammatory inspection. The molecular modeling and docking studies indicated high affinity of 2,4-D toward COX-2 enzyme in a way similar to Ibuprofen, suggesting a higher anti-inflammatory activity. Molecular docking by both MOE 2013.08 and Leadit 2.1.2 revealed excellent binding pattern compared to some of well-known non-steroidal anti-inflammatory drugs. 2,4-D was formulated in different gel bases. In vitro drug release experiments were used to examine the best 2,4-D formula for in vivo studies. In vivo carrageenan-induced hind paw edema inflammatory model in rats was used to test the in silico finding. 2,4-D showed potential in vivo anti-inflammatory activity and significantly reduced the concentration of prostaglandin E2 in hind paw tissues in a way similar to Ibuprofen. These results may open the door to introduce a new anti-inflammatory molecule; especially that 2,4-D is a well-investigated regarding its toxicity and side effect. PMID:25245006

  14. Detection of cis- and trans-acting Factors in DNA Structure-Induced Genetic Instability Using In silico and Cellular Approaches.

    PubMed

    Wang, Guliang; Zhao, Junhua; Vasquez, Karen M

    2016-01-01

    Sequences that can adopt alternative DNA structures (i.e., non-B DNA) are very abundant in mammalian genomes, and recent studies have revealed many important biological functions of non-B DNA structures in chromatin remodeling, DNA replication, transcription, and genetic instability. Here, we provide results from an in silico web-based search engine coupled with cell-based experiments to characterize the roles of non-B DNA conformations in genetic instability in eukaryotes. The purpose of this article is to illustrate strategies that can be used to identify and interrogate the biological roles of non-B DNA structures, particularly on genetic instability. We have included unpublished data using a short H-DNA-forming sequence from the human c-MYC promoter region as an example, and identified two different mechanisms of H-DNA-induced genetic instability in yeast and mammalian cells: a DNA replication-related model of mutagenesis; and a replication-independent cleavage model. Further, we identified candidate proteins involved in H-DNA-induced genetic instability by using a yeast genetic screen. A combination of in silico and cellular methods, as described here, should provide further insight into the contributions of non-B DNA structures in biological functions, genetic evolution, and disease development. PMID:27532010

  15. A thiamin-bound, pre-decarboxylation reaction intermediate analogue in the pyruvate dehydrogenase E1 subunit induces large scale disorder-to-order transformations in the enzyme and reveals novel structural features in the covalently bound adduct.

    PubMed

    Arjunan, Palaniappa; Sax, Martin; Brunskill, Andrew; Chandrasekhar, Krishnamoorthy; Nemeria, Natalia; Zhang, Sheng; Jordan, Frank; Furey, William

    2006-06-01

    The crystal structure of the E1 component from the Escherichia coli pyruvate dehydrogenase multienzyme complex (PDHc) has been determined with phosphonolactylthiamin diphosphate (PLThDP) in its active site. PLThDP serves as a structural and electrostatic analogue of the natural intermediate alpha-lactylthiamin diphosphate (LThDP), in which the carboxylate from the natural substrate pyruvate is replaced by a phosphonate group. This represents the first example of an experimentally determined, three-dimensional structure of a thiamin diphosphate (ThDP)-dependent enzyme containing a covalently bound, pre-decarboxylation reaction intermediate analogue and should serve as a model for the corresponding intermediates in other ThDP-dependent decarboxylases. Regarding the PDHc-specific reaction, the presence of PLThDP induces large scale conformational changes in the enzyme. In conjunction with the E1-PLThDP and E1-ThDP structures, analysis of a H407A E1-PLThDP variant structure shows that an interaction between His-407 and PLThDP is essential for stabilization of two loop regions in the active site that are otherwise disordered in the absence of intermediate analogue. This ordering completes formation of the active site and creates a new ordered surface likely involved in interactions with the lipoyl domains of E2s within the PDHc complex. The tetrahedral intermediate analogue is tightly held in the active site through direct hydrogen bonds to residues His-407, Tyr-599, and His-640 and reveals a new, enzyme-induced, strain-related feature that appears to aid in the decarboxylation process. This feature is almost certainly present in all ThDP-dependent decarboxylases; thus its inclusion in our understanding of general thiamin catalysis is important. PMID:16531404

  16. Network modelling reveals the mechanism underlying colitis-associated colon cancer and identifies novel combinatorial anti-cancer targets.

    PubMed

    Lu, Junyan; Zeng, Hanlin; Liang, Zhongjie; Chen, Limin; Zhang, Liyi; Zhang, Hao; Liu, Hong; Jiang, Hualiang; Shen, Bairong; Huang, Ming; Geng, Meiyu; Spiegel, Sarah; Luo, Cheng

    2015-01-01

    The connection between inflammation and tumourigenesis has been well established. However, the detailed molecular mechanism underlying inflammation-associated tumourigenesis remains unknown because this process involves a complex interplay between immune microenvironments and epithelial cells. To obtain a more systematic understanding of inflammation-associated tumourigenesis as well as to identify novel therapeutic approaches, we constructed a knowledge-based network describing the development of colitis-associated colon cancer (CAC) by integrating the extracellular microenvironment and intracellular signalling pathways. Dynamic simulations of the CAC network revealed a core network module, including P53, MDM2, and AKT, that may govern the malignant transformation of colon epithelial cells in a pro-tumor inflammatory microenvironment. Furthermore, in silico mutation studies and experimental validations led to a novel finding that concurrently targeting ceramide and PI3K/AKT pathway by chemical probes or marketed drugs achieves synergistic anti-cancer effects. Overall, our network model can guide further mechanistic studies on CAC and provide new insights into the design of combinatorial cancer therapies in a rational manner. PMID:26446703

  17. Network modelling reveals the mechanism underlying colitis-associated colon cancer and identifies novel combinatorial anti-cancer targets

    PubMed Central

    Lu, Junyan; Zeng, Hanlin; Liang, Zhongjie; Chen, Limin; Zhang, Liyi; Zhang, Hao; Liu, Hong; Jiang, Hualiang; Shen, Bairong; Huang, Ming; Geng, Meiyu; Spiegel, Sarah; Luo, Cheng

    2015-01-01

    The connection between inflammation and tumourigenesis has been well established. However, the detailed molecular mechanism underlying inflammation-associated tumourigenesis remains unknown because this process involves a complex interplay between immune microenvironments and epithelial cells. To obtain a more systematic understanding of inflammation-associated tumourigenesis as well as to identify novel therapeutic approaches, we constructed a knowledge-based network describing the development of colitis-associated colon cancer (CAC) by integrating the extracellular microenvironment and intracellular signalling pathways. Dynamic simulations of the CAC network revealed a core network module, including P53, MDM2, and AKT, that may govern the malignant transformation of colon epithelial cells in a pro-tumor inflammatory microenvironment. Furthermore, in silico mutation studies and experimental validations led to a novel finding that concurrently targeting ceramide and PI3K/AKT pathway by chemical probes or marketed drugs achieves synergistic anti-cancer effects. Overall, our network model can guide further mechanistic studies on CAC and provide new insights into the design of combinatorial cancer therapies in a rational manner. PMID:26446703

  18. Global Characteristics of School Transformation in China

    ERIC Educational Resources Information Center

    Harris, Jessica; Zhao, Yong; Caldwell, Brian J.

    2009-01-01

    In many ways, China's education system is quite different from systems of education in the West. Rich descriptions of school transformation, however, have revealed that the factors that fuelled transformation in schools in China are also evident in schools in Australia, England, Finland, Wales and the United States. This paper draws on an…

  19. Transformation Analysis of Russian Instrumental Constructions.

    ERIC Educational Resources Information Center

    Worth, Dean Stoddard

    1958-01-01

    This comparative study of traditional and transformational approaches to the syntax of standard Russian proposes the superiority of analysis in terms of possible and impossible transformations, thereby revealing the existence of a level of linguistic form superior to that of simple morphophonemic description. Five classes of word-combinations of…

  20. The Process of Transformation: Steps toward Change.

    ERIC Educational Resources Information Center

    Tarule, Jill Mattuck

    1980-01-01

    A study of adult learners reveals four steps of transformative change in adult life: diffusion, dissonance, differentiation, and coherence. The educational implications of these steps are explored through case studies, and it is argued that these transformative changes affect not only the individual and the nature of adult education, but the…

  1. In vivo and in silico analyses of estrogenic potential of bisphenol analogs in medaka (Oryzias latipes) and common carp (Cyprinus carpio).

    PubMed

    Yamaguchi, Akemi; Ishibashi, Hiroshi; Arizono, Koji; Tominaga, Nobuaki

    2015-10-01

    Various studies have demonstrated the estrogenic effect of bisphenol A (BPA), a member of bisphenol analogs (BPs), in in vitro and in vivo assays. However, limited data are available on the estrogenic potentials and risks of other BPs in aquatic organisms. In addition, the estrogenic effect of chemicals is known to have species-specific responses in teleost fish. The objective of this study was to evaluate the potential estrogenic effects of BPs on the medaka (Oryzias latipes) and common carp (Cyprinus carpio) using in vivo and in silico assays. Our quantitative real-time PCR analyses revealed that the expression levels of several hepatic estrogen-responsive biomarker genes in male medaka responded to various types and concentrations of BPs in a dose-response manner. The order of in vivo estrogenic potencies of BPs was as follows: BPC≈BPAF>BPB>BPA⋙BPP. To further investigate the interaction potential of BPs with medaka estrogen receptor α (ERα) in silico, a three-dimensional model of the ERα ligand-binding domain (LBD) was built and docking simulations were performed. The docking simulation analysis revealed that BPC interaction potential for medaka ERα LBD was the most potent, followed by BPAF and BPA. Comparing this with carp ERα LBD revealed that the interaction potentials of these BPs to medaka ERα LBD were more stable than to carp ERα LBD. Furthermore, we identified key amino acid residues in medaka ERα LBD that interacted with BPC (Glu356, Arg397, and Cys533), BPAF (Thr350 and Glu356), and BPA (Glu356 and Met424), and found some differences in these key amino acid residues between medaka and carp ERα LBDs. These results of in vivo and in silico analyses showed potential estrogenic effects of BPs in teleost fish, and they also indicated that the differences in interaction potentials and key amino acid residues between medaka and carp ERα LBDs may be due to the differences between the species and estrogenic potencies of the selected BPs. PMID

  2. Novel G-quadruplex stabilizing agents: in-silico approach and dynamics.

    PubMed

    Kar, Rajiv Kumar; Suryadevara, Priyanka; Jana, Jagannath; Bhunia, Anirban; Chatterjee, Subhrangsu

    2013-12-01

    The stabilization of overhang G-rich repetitive DNA units at the 3'-end of telomeres, which are well known to form functionally important G-quadruplex structures, is a current goal in designing novel anticancer drugs. In the present study, we have undertaken an in silico approach by molecular docking using a small molecule library to find potential G-quadruplex stabilizing agents. Two molecules, A, [N'1-imino(2-pyridyl)methyl-3,4,5-trimethoxybenzene-1-carbohydrazide] and B, [(3-[4-({[3-({4-[(2cyanoethyl)(methyl)amino]benzylidene}amino)propyl]imino}methyl)(methyl) anilino]propanenitrile)], that had good docking scores have been investigated for interaction with G-quadruplexes in a Molecular Dynamics simulation study. Fluorescence spectroscopy of G-quadruplexes bound to the screened molecules A and B was used to experimentally validate the theoretical results. The binding of ligands A and B to G-quadruplexes resulted in blue shifts of 10-18 nm, respectively, in the fluorescence emission spectra of the G-quadruplexes, demonstrating that both molecules bind to the G-face of the quadruplex. The same experiment was performed for the complexation of these small molecules with a G-rich DNA duplex, [Formula: see text]. Interestingly, no blue shift was observed in the fluorescence emission spectra of the DNA duplex in the presence of these small molecules. Thus, these findings indicated that these ligands very selectively bind to G-quadruplexes instead of the duplex DNA. In addition, a one-dimensional water ligand observed via a gradient spectroscopy Nuclear Magnetic Resonance (NMR) experiment showed that both molecules bound to the 23-mer G-quadruplex DNA. The molecular properties of the ligand-quadruplex complex have been analyzed with the help of the Adaptive Poisson-Boltzmann Solver, revealing that electrostatics govern the binding of the small molecules to G-quadruplexes. Both molecules were investigated in detail using solvation free energy calculations and

  3. Eukaryotic signature proteins of Prosthecobacter dejongeii and Gemmata sp. Wa-1 as revealed by in silico analysis.

    PubMed

    Staley, James T; Bouzek, Heather; Jenkins, Cheryl

    2005-02-01

    The genomes of representatives of three bacterial phyla have been compared with the list of 347 eukaryotic signature proteins (ESPs) derived by Hartman and Fedorov [Proc. Natl. Acad. Sci. USA 99 (2002) 1420]. The species included Prosthecobacter dejongeii of the Verrucomicrobia phylum, Gemmata sp. Wa-1 of the Planctomycetes phylum and Caulobacter crescentus of the Proteobacteria. The protist Trypanosoma brucei was used as a eukaryotic control. P. dejongeii had unique ERGO blast matches to alpha-, beta-, and gamma-tubulin, to Set2, a transcriptional factor associated with eukaryotic DNA, and to LAMMER protein kinase for a total of 10 high-scoring ESP matches altogether. Gemmata sp. Wa-1 shared four of its 17 high-scoring ESP matches with P. dejongeii, and that information coupled with other genomic data provides strong support that these two phyla are related to one another. If the ESP list is an accurate listing of unique eukaryotic proteins, then the low number of high-scoring matches between the proteins of these two bacteria with the list raises doubts about these phyla being direct ancestors of the Eucarya. However, this does not rule out the possibility that ancestral members of either the Verrucomicrobia or Planctomycetes may have played an important role in the evolution of a proto-eukaryotic organism. PMID:15667994

  4. In silico Investigation of the PglB Active Site Reveals Transient Catalytic States and Octahedral Metal Ion Coordination.

    PubMed

    Pedebos, Conrado; Arantes, Pablo Ricardo; Giesel, Guilherme Menegon; Verli, Hugo

    2015-11-01

    The last step of the bacterial N-glycosylation pathway involves PglB, an oligosaccharyltransferase, which is responsible for the en bloc transfer of a fully assembled oligosaccharide chain to a protein possessing the extended motif D/E-X-N-X-S/T. Recently, this molecule had its full structure elucidated, enabling the description of its domains and the proposition of a catalytic mechanism. By employing molecular dynamics simulations, we were able to evaluate structural aspects of PglB, suggesting prevalent motions that may bring insights into the mechanism of the glycosylated peptide detachment. Additionally, we identified transient states at the catalytic site, in which the previously described carboxamide twisting mechanism was observed. Aided by quantum mechanics calculations for each different conformational states of the catalytic site, we determined the presence of an octahedral metal coordination, along with the presence of one water molecule at the catalytic site. PMID:26220543

  5. Fathead Minnow Steroidogenesis: In Silico Analyses Reveals Tradeoffs Between Nominal Target Efficacy and Robustness to Cross-talk

    EPA Science Inventory

    This paper presents the formulation and evaluation of a mechanistic mathematical model of fathead minnow ovarian steroidogenesis. The model presented in the present study was adpated from other models developed as part of an integrated, multi-disciplinary computational toxicolog...

  6. In silico simulation modeling reveals the importance of the Casparian strip for efficient silicon uptake in rice roots.

    PubMed

    Sakurai, Gen; Satake, Akiko; Yamaji, Naoki; Mitani-Ueno, Namiki; Yokozawa, Masayuki; Feugier, François Gabriel; Ma, Jian Feng

    2015-04-01

    Silicon (Si) uptake by the roots is mediated by two different transporters, Lsi1 (passive) and Lsi2 (active), in rice (Oryza sativa). Both transporters are polarly localized in the plasma membranes of exodermal (outer) and endodermal (inner) cells with Casparian strips. However, it is unknown how rice is able to take up large amounts of Si compared with other plants, and why rice Si transporters have a characteristic cellular localization pattern. To answer these questions, we simulated Si uptake by rice roots by developing a mathematical model based on a simple diffusion equation that also accounts for active transport by Lsi2. In this model, we calibrated the model parameters using in vivo experimental data on the Si concentrations in the xylem sap and a Monte Carlo method. In our simulation experiments, we compared the Si uptake between roots with various transporter and Casparian strip locations and estimated the Si transport efficiency of roots with different localization patterns and quantities of the Lsi transporters. We found that the Si uptake by roots that lacked Casparian strips was lower than that of normal roots. This suggests that the double-layer structure of the Casparian strips is an important factor in the high Si uptake by rice. We also found that among various possible localization patterns, the most efficient one was that of the wild-type rice; this may explain the high Si uptake capacity of rice. PMID:25673476

  7. Fathead minnow steroidogenesis: in silico analyses reveals tradeoffs between nominal target efficacy and robustness to cross-talk

    PubMed Central

    2010-01-01

    Background Interpreting proteomic and genomic data is a major challenge in predictive ecotoxicology that can be addressed by a systems biology approach. Mathematical modeling provides an organizational platform to consolidate protein dynamics with possible genomic regulation. Here, a model of ovarian steroidogenesis in the fathead minnow, Pimephales promelas, (FHM) is developed to evaluate possible transcriptional regulation of steroid production observed in microarray studies. Results The model was developed from literature sources, integrating key signaling components (G-protein and PKA activation) with their ensuing effect on steroid production. The model properly predicted trajectory behavior of estradiol and testosterone when fish were exposed to fadrozole, a specific aromatase inhibitor, but failed to predict the steroid hormone behavior occurring one week post-exposure as well as the increase in steroid levels when the stressor was removed. In vivo microarray data implicated three modes of regulation which may account for over-production of steroids during a depuration phase (when the stressor is removed): P450 enzyme up-regulation, inhibin down-regulation, and luteinizing hormone receptor up-regulation. Simulation studies and sensitivity analysis were used to evaluate each case as possible source of compensation to endocrine stress. Conclusions Simulation studies of the testosterone and estradiol response to regulation observed in microarray data supported the hypothesis that the FHM steroidogenesis network compensated for endocrine stress by modulating the sensitivity of the ovarian network to global cues coming from the hypothalamus and pituitary. Model predictions of luteinizing hormone receptor regulation were consistent with depuration and in vitro data. These results challenge the traditional approach to network elucidation in systems biology. Generally, the most sensitive interactions in a network are targeted for further elucidation but microarray evidence shows that homeostatic regulation of the steroidogenic network is likely maintained by a mildly sensitive interaction. We hypothesize that effective network elucidation must consider both the sensitivity of the target as well as the target's robustness to biological noise (in this case, to cross-talk) when identifying possible points of regulation. PMID:20579396

  8. Restoration of optimal ellipsoid left ventricular geometry: lessons learnt from in silico surgical modelling

    PubMed Central

    Adhyapak, Srilakshmi M.; Menon, Prahlad G.; Rao Parachuri, V.

    2014-01-01

    OBJECTIVES Several issues that are inherent in the surgical techniques of surgical ventricular restoration (SVR) need specialized devices or techniques to overcome them, which may not always result in optimal outcomes. We used a non-invasive novel in silico modelling technique to study left ventricular (LV) morphology and function before and after SVR. The cardiac magnetic resonance imaging derived actual pre- and postoperative endocardial morphology and function was compared with the in silico analysis of the same. METHODS Cardiac magnetic resonance steady state free precession (SSFP) cine images were employed to segment endocardial surface contours over the cardiac cycle. Using the principle of Hausdorff distance to examine phase-to-phase regional endocardial displacement, dyskinetic/akinetic areas were identified at the instant of peak basal contraction velocity. Using a three-dimensional (3D) surface clipping tool, the maximally scarred, dyskinetic or akinetic LV antero-apical areas were virtually resected and a new apex was created. A virtual rectangular patch was created upon the clipped surface LV model by 3D Delaunay triangulation. Presurgical endocardial mechanical function quantified from cine cardiac magnetic resonance, using a technique of spherical harmonics (SPHARM) surface parameterization, was applied onto the virtually clipped and patched LV surface model. Finally, the in silico model of post-SVR LV shape was analysed for quantification of regional left ventricular volumes (RLVVs) and function. This was tested in 2 patients with post-myocardial infarction antero-apical LV aneuryms. Left ventricular mechanical dysynchrony was evaluated by RLVV analysis of pre-SVR, in silico post-SVR and actual post-SVR LV endocardial surface data. RESULTS Following exclusion of the scarred areas, the virtual resected LV model demonstrated significantly lesser areas of akinesia. The decreases in regional LV volumes in the in silico modelling were significant and

  9. In Silico Model-Driven Assessment of the Effects of Single Nucleotide Polymorphisms (SNPs) on Human Red Blood Cell Metabolism

    PubMed Central

    Jamshidi, Neema; Wiback, Sharon J.; Palsson, Bernhard Ø.

    2002-01-01

    The completion of the human genome project and the construction of single nucleotide polymorphism (SNP) maps have lead to significant efforts to find SNPs that can be linked to pathophysiology. In silico models of complete biochemical reaction networks relate a cell's individual reactions to the function of the entire network. Sequence variations can in turn be related to kinetic properties of individual enzymes, thus allowing an in silico model-driven assessment of the effects of defined SNPs on overall cellular functions. This process is applied to defined SNPs in two key enzymes of human red blood cell metabolism: glucose-6-phosphate dehydrogenase and pyruvate kinase. The results demonstrate the utility of in silico models in providing insight into differences between red cell function in patients with chronic and nonchronic anemia. In silico models of complex cellular processes are thus likely to aid in defining and understanding key SNPs in human pathophysiology. PMID:12421755

  10. Characterization of metabolic interrelationships and in silico phenotyping of lipoprotein particles using self-organizing maps[S

    PubMed Central

    Kumpula, Linda S.; Mäkelä, Sanna M.; Mäkinen, Ville-Petteri; Karjalainen, Anna; Liinamaa, Johanna M.; Kaski, Kimmo; Savolainen, Markku J.; Hannuksela, Minna L.; Ala-Korpela, Mika

    2010-01-01

    Plasma lipid concentrations cannot properly account for the complex interactions prevailing in lipoprotein (patho)physiology. Sequential ultracentrifugation (UCF) is the gold standard for physical lipoprotein isolations allowing for subsequent analyses of the molecular composition of the particles. Due to labor and cost issues, however, the UCF-based isolations are usually done only for VLDL, LDL, and HDL fractions; sometimes with the addition of intermediate density lipoprotein (IDL) particles and the fractionation of HDL into HDL2 and HDL3 (as done here; n = 302). We demonstrate via these data, with the lipoprotein lipid concentration and composition information combined, that the self-organizing map (SOM) analysis reveals a novel data-driven in silico phenotyping of lipoprotein metabolism beyond the experimentally available classifications. The SOM-based findings are biologically consistent with several well-known metabolic characteristics and also explain some apparent contradictions. The novelty is the inherent emergence of complex lipoprotein associations; e.g., the metabolic subgrouping of the associations between plasma LDL cholesterol concentrations and the structural subtypes of LDL particles. Importantly, lipoprotein concentrations cannot pinpoint lipoprotein phenotypes. It would generally be beneficial to computationally enhance the UCF-based lipoprotein data as illustrated here. Particularly, the compositional variations within the lipoprotein particles appear to be a fundamental issue with metabolic and clinical corollaries. PMID:19734566

  11. Design, synthesis, in silico toxicity prediction, molecular docking, and evaluation of novel pyrazole derivatives as potential antiproliferative agents

    PubMed Central

    Ravula, Parameshwar; Vamaraju, Harinadha Babu; Paturi, Manichandrika; Chandra JN, Narendra Sharath; Kolli, Swetha

    2016-01-01

    A new series of pyrazole derivatives were designed by docking into vascular endothelial growth factor receptor-2 (VEGFR-2) kinase active site. The designed compounds were synthesized and evaluated for in vitro antiproliferative activity against HT-29 colon and PC-3 prostate cancer cell lines, and angioinhibitory activity in chorioallantoic membrane (CAM) model. Based on the obtained antiproliferative activity results of in vitro and CAM assay, compounds 4b, 4c, 4f, 5b, 5c and 5f were selected, and tested for anticancer activity using in vivo ehrlich ascites carcinoma (EAC) bearing mice. Compound 5c showed the highest in vitro antiproliferative activity against HT-29 and PC-3 with IC50 values of 6.43 µM and 9.83 µM respectively and comparable to reference drug Doxorubicin. Results of in vivo anticancer activity revealed that compound 5c showed the highest percentage increase in life span ( %ILS), and mean survival time (MST) with 75.13 % and 32.4 ± 0.53 days respectively. Moreover, compound 5c demonstrated significant reduction of microvessel density (MVD) in CAM assay. In silico prediction of toxicities, and drug score profiles of designed compounds are promising. A correlation made between the results obtained by antiproliferative study and molecular docking studies suggest that the synthesized compounds may be beneficial as molecular scaffolds for antiproliferative activity. PMID:27103897

  12. Structural insights into the interaction between molluscan hemocyanins and phenolic substrates: An in silico study using docking and molecular dynamics.

    PubMed

    Naresh, K N; Sreekumar, Arun; Rajan, S S

    2015-09-01

    Hemocyanin is a multimeric type-3 copper containing oxygen carrier protein that exhibits phenoloxidase-like activity and is found in selected species of arthropoda and mollusca. The phenoloxidase activity in the molluscan hemocyanins can be triggered by the proteolytic removal of the C-terminal β-rich sandwich domain of the protein or by the treatment with chemical agents like SDS, both of which enable active site access to the phenolic substrates. The mechanism by which SDS treatment enhances active site access to the substrates is however not well understood in molluscan hemocyanins. Here, using a combination of in silico molecular dynamics (MD) and docking studies on the crystal structure of Octopus dofleini hemocyanin (PDB code:1JS8), we demonstrate that the C-terminal β-domain of the protein plays a crucial role in regulating active site access to bulky phenolic substrates. Furthermore, MD simulation of hemocyanin in SDS revealed displacement of β-domain, enhanced active site access and a resulting increase in binding affinity for substrates. These observations were further validated by enzyme kinetics experiments. PMID:26300244

  13. Design, synthesis, in silico toxicity prediction, molecular docking, and evaluation of novel pyrazole derivatives as potential antiproliferative agents.

    PubMed

    Ravula, Parameshwar; Vamaraju, Harinadha Babu; Paturi, Manichandrika; Chandra Jn, Narendra Sharath; Kolli, Swetha

    2016-01-01

    A new series of pyrazole derivatives were designed by docking into vascular endothelial growth factor receptor-2 (VEGFR-2) kinase active site. The designed compounds were synthesized and evaluated for in vitro antiproliferative activity against HT-29 colon and PC-3 prostate cancer cell lines, and angioinhibitory activity in chorioallantoic membrane (CAM) model. Based on the obtained antiproliferative activity results of in vitro and CAM assay, compounds 4b, 4c, 4f, 5b, 5c and 5f were selected, and tested for anticancer activity using in vivo ehrlich ascites carcinoma (EAC) bearing mice. Compound 5c showed the highest in vitro antiproliferative activity against HT-29 and PC-3 with IC50 values of 6.43 µM and 9.83 µM respectively and comparable to reference drug Doxorubicin. Results of in vivo anticancer activity revealed that compound 5c showed the highest percentage increase in life span ( %ILS), and mean survival time (MST) with 75.13 % and 32.4 ± 0.53 days respectively. Moreover, compound 5c demonstrated significant reduction of microvessel density (MVD) in CAM assay. In silico prediction of toxicities, and drug score profiles of designed compounds are promising. A correlation made between the results obtained by antiproliferative study and molecular docking studies suggest that the synthesized compounds may be beneficial as molecular scaffolds for antiproliferative activity. PMID:27103897

  14. Peptides derived from CXCL8 based on in silico analysis inhibit CXCL8 interactions with its receptor CXCR1

    NASA Astrophysics Data System (ADS)

    Jiang, Shinn-Jong; Liou, Je-Wen; Chang, Chun-Chun; Chung, Yi; Lin, Lee-Fong; Hsu, Hao-Jen

    2015-12-01

    Chemokine CXCL8 is crucial for regulation of inflammatory and immune responses via activating its cognate receptor CXCR1. In this study, molecular docking and binding free energy calculations were combined to predict the initial binding event of CXCL8 to CXCR1 for peptide drug design. The simulations reveal that in the initial binding, the N-loop of CXCL8 interacts with the N-terminus of CXCR1, which is dominated by electrostatic interactions. The derived peptides from the binding region of CXCL8 are synthesized for further confirmation. Surface plasmon resonance analyses indicate that the CXCL8 derived peptide with 14 residues is able to bind to the receptor CXCR1 derived peptide with equilibrium KD of 252 μM while the peptide encompassing a CXCL8 K15A mutation hardly binds to CXCR1 derived peptide (KD = 1553 μM). The cell experiments show that the designed peptide inhibits CXCL8-induced and LPS-activated monocytes adhesion and transmigration. However, when the peptides were mutated on two lysine residues (K15 and K20), the inhibition effects were greatly reduced indicating these two amino acids are key residues for the initial binding of CXCL8 to CXCR1. This study demonstrates that in silico prediction based functional peptide design can be effective for developing anti-inflammation drugs.

  15. Peptides derived from CXCL8 based on in silico analysis inhibit CXCL8 interactions with its receptor CXCR1.

    PubMed

    Jiang, Shinn-Jong; Liou, Je-Wen; Chang, Chun-Chun; Chung, Yi; Lin, Lee-Fong; Hsu, Hao-Jen

    2015-01-01

    Chemokine CXCL8 is crucial for regulation of inflammatory and immune responses via activating its cognate receptor CXCR1. In this study, molecular docking and binding free energy calculations were combined to predict the initial binding event of CXCL8 to CXCR1 for peptide drug design. The simulations reveal that in the initial binding, the N-loop of CXCL8 interacts with the N-terminus of CXCR1, which is dominated by electrostatic interactions. The derived peptides from the binding region of CXCL8 are synthesized for further confirmation. Surface plasmon resonance analyses indicate that the CXCL8 derived peptide with 14 residues is able to bind to the receptor CXCR1 derived peptide with equilibrium KD of 252 μM while the peptide encompassing a CXCL8 K15A mutation hardly binds to CXCR1 derived peptide (KD = 1553 μM). The cell experiments show that the designed peptide inhibits CXCL8-induced and LPS-activated monocytes adhesion and transmigration. However, when the peptides were mutated on two lysine residues (K15 and K20), the inhibition effects were greatly reduced indicating these two amino acids are key residues for the initial binding of CXCL8 to CXCR1. This study demonstrates that in silico prediction based functional peptide design can be effective for developing anti-inflammation drugs. PMID:26689258

  16. In silico-screening approaches for lead generation: identification of novel allosteric modulators of human-erythrocyte pyruvate kinase.

    PubMed

    Tripathi, Ashutosh; Safo, Martin K

    2012-01-01

    Identification of allosteric binding site modulators have gained increased attention lately for their potential to be developed as selective agents with a novel chemotype and targeting perhaps a new and unique binding site with probable fewer side effects. Erythrocyte pyruvate kinase (R-PK) is an important glycolytic enzyme that can be pharmacologically modulated through its allosteric effectors for the treatment of hemolytic anemia, sickle-cell anemia, hypoxia-related diseases, and other disorders arising from erythrocyte PK malfunction. An in-silico screening approach was applied to identify novel allosteric modulators of pyruvate kinase. A small-molecules database of the National Cancer Institute (NCI), was virtually screened based on structure/ligand-based pharmacophore. The virtual screening campaign led to the identification of several compounds with similar pharmacophoric features as fructose-1,6-bisphosphate (FBP), the natural allosteric activator of the kinase. The compounds were subsequently docked into the FBP-binding site using the programs FlexX and GOLD, and their interactions with the protein were analyzed with the energy-scoring function of HINT. Seven promising candidates were obtained from the NCI and subjected to kinetics analysis, which revealed both activators and inhibitors of the R-isozyme of PK (R-PK). PMID:22052500

  17. In silico Neuropeptidome of Female Macrobrachium rosenbergii Based on Transcriptome and Peptide Mining of Eyestalk, Central Nervous System and Ovary

    PubMed Central

    Wang, Tianfang; Zhao, Min; Elizur, Abigail; Sretarugsa, Prapee; Cummins, Scott F.; Sobhon, Prasert

    2015-01-01

    Macrobrachium rosenbergii is the most economically important of the cultured freshwater crustacean species, yet there is currently a deficiency in genomic and transcriptomic information for research requirements. In this study, we present an in silico analysis of neuropeptide genes within the female M. rosenbergii eyestalk, central nervous system, and ovary. We could confidently predict 37 preproneuropeptide transcripts, including those that encode bursicons, crustacean cardioactive peptide, crustacean hyperglycemic hormones, eclosion hormone, pigment-dispersing hormones, diuretic hormones, neuropeptide F, neuroparsins, SIFamide, and sulfakinin. These transcripts are most prominent within the eyestalk and central nervous system. Transcript tissue distribution as determined by reverse transcription-polymerase chain reaction revealed the presence of selected neuropeptide genes of interest mainly in the nervous tissues while others were additionally present in the non-nervous tissues. Liquid chromatography-mass spectrometry analysis of eyestalk peptides confirmed the presence of the crustacean hyperglycemic hormone precursor. This data set provides a strong foundation for further studies into the functional roles of neuropeptides in M. rosenbergii, and will be especially helpful for developing methods to improve crustacean aquaculture. PMID:26023789

  18. In silico Identification of Ergosterol as a Novel Fungal Metabolite Enhancing RuBisCO Activity in Lycopersicum esculentum.

    PubMed

    Mitra, Joyeeta; Narad, Priyanka; Sengupta, Abhishek; Sharma, P D; Paul, P K

    2016-09-01

    RuBisCO (EC 4.1.1.39), a key enzyme found in stroma of chloroplast, is important for fixing atmospheric CO2 in plants. Alterations in the activity of RuBisCO could influence photosynthetic yield. Therefore, to understand the activity of the protein, knowledge about its structure is pertinent. Though the structure of Nicotiana RuBisCO has been modeled, the structure of tomato RuBisCO is still unknown. RuBisCO extracted from chloroplasts of tomato leaves was subjected to MALDI-TOF-TOF followed by Mascot Search. The protein sequence based on gene identification numbers was subjected to in silico model construction, characterization and docking studies. The primary structure analysis revealed that protein was stable, neutral, hydrophilic and has an acidic pI. The result though indicates a 90 % homology with other members of Solanaceae but differs from the structure of Arabidopsis RuBisCO. Different ligands were docked to assess the activity of RuBisCO against these metabolite components. Out of the number of modulators tested, ergosterol had the maximum affinity (E = -248.08) with RuBisCO. Ergosterol is a major cell wall component of fungi and has not been reported to be naturally found in plants. It is a known immune elicitor in plants. The current study throws light on its role in affecting RuBisCO activity in plants, thereby bringing changes in the photosynthetic rate. PMID:26253718

  19. Peptides derived from CXCL8 based on in silico analysis inhibit CXCL8 interactions with its receptor CXCR1

    PubMed Central

    Jiang, Shinn-Jong; Liou, Je-Wen; Chang, Chun-Chun; Chung, Yi; Lin, Lee-Fong; Hsu, Hao-Jen

    2015-01-01

    Chemokine CXCL8 is crucial for regulation of inflammatory and immune responses via activating its cognate receptor CXCR1. In this study, molecular docking and binding free energy calculations were combined to predict the initial binding event of CXCL8 to CXCR1 for peptide drug design. The simulations reveal that in the initial binding, the N-loop of CXCL8 interacts with the N-terminus of CXCR1, which is dominated by electrostatic interactions. The derived peptides from the binding region of CXCL8 are synthesized for further confirmation. Surface plasmon resonance analyses indicate that the CXCL8 derived peptide with 14 residues is able to bind to the receptor CXCR1 derived peptide with equilibrium KD of 252 μM while the peptide encompassing a CXCL8 K15A mutation hardly binds to CXCR1 derived peptide (KD = 1553 μM). The cell experiments show that the designed peptide inhibits CXCL8-induced and LPS-activated monocytes adhesion and transmigration. However, when the peptides were mutated on two lysine residues (K15 and K20), the inhibition effects were greatly reduced indicating these two amino acids are key residues for the initial binding of CXCL8 to CXCR1. This study demonstrates that in silico prediction based functional peptide design can be effective for developing anti-inflammation drugs. PMID:26689258

  20. In silico modification of suberoylanilide hydroxamic acid (SAHA) as potential inhibitor for class II histone deacetylase (HDAC)

    PubMed Central

    2011-01-01

    Background The cervical cancer is the second most prevalent cancer for the woman in the world. It is caused by the oncogenic human papilloma virus (HPV). The inhibition activity of histone deacetylase (HDAC) is a potential strategy for cancer therapy. Suberoylanilide hydroxamic acid (SAHA) is widely known as a low toxicity HDAC inhibitor. This research presents in silico SAHA modification by utilizing triazole, in order to obtain a better inhibitor. We conducted docking of the SAHA inhibitor and 12 modified versions to six class II HDAC enzymes, and then proceeded with drug scanning of each one of them. Results The docking results show that the 12 modified inhibitors have much better binding affinity and inhibition potential than SAHA. Based on drug scan analysis, six of the modified inhibitors have robust pharmacological attributes, as revealed by drug likeness, drug score, oral bioavailability, and toxicity levels. Conclusions The binding affinity, free energy and drug scan screening of the best inhibitors have shown that 1c and 2c modified inhibitors are the best ones to inhibit class II HDAC. PMID:22373132

  1. In Silico Design and Experimental Validation of siRNAs Targeting Conserved Regions of Multiple Hepatitis C Virus Genotypes

    PubMed Central

    ElHefnawi, Mahmoud; Kim, TaeKyu; Kamar, Mona A.; Min, Saehong; Hassan, Nafisa M.; El-Ahwany, Eman; Kim, Heeyoung; Zada, Suher; Amer, Marwa; Windisch, Marc P.

    2016-01-01

    RNA interference (RNAi) is a post-transcriptional gene silencing mechanism that mediates the sequence-specific degradation of targeted RNA and thus provides a tremendous opportunity for development of oligonucleotide-based drugs. Here, we report on the design and validation of small interfering RNAs (siRNAs) targeting highly conserved regions of the hepatitis C virus (HCV) genome. To aim for therapeutic applications by optimizing the RNAi efficacy and reducing potential side effects, we considered different factors such as target RNA variations, thermodynamics and accessibility of the siRNA and target RNA, and off-target effects. This aim was achieved using an in silico design and selection protocol complemented by an automated MysiRNA-Designer pipeline. The protocol included the design and filtration of siRNAs targeting highly conserved and accessible regions within the HCV internal ribosome entry site, and adjacent core sequences of the viral genome with high-ranking efficacy scores. Off-target analysis excluded siRNAs with potential binding to human mRNAs. Under this strict selection process, two siRNAs (HCV353 and HCV258) were selected based on their predicted high specificity and potency. These siRNAs were tested for antiviral efficacy in HCV genotype 1 and 2 replicon cell lines. Both in silico-designed siRNAs efficiently inhibited HCV RNA replication, even at low concentrations and for short exposure times (24h); they also exceeded the antiviral potencies of reference siRNAs targeting HCV. Furthermore, HCV353 and HCV258 siRNAs also inhibited replication of patient-derived HCV genotype 4 isolates in infected Huh-7 cells. Prolonged treatment of HCV replicon cells with HCV353 did not result in the appearance of escape mutant viruses. Taken together, these results reveal the accuracy and strength of our integrated siRNA design and selection protocols. These protocols could be used to design highly potent and specific RNAi-based therapeutic oligonucleotide

  2. In silico design, cloning and high level expression of L7/L12-TOmp31 fusion protein of Brucella antigens

    PubMed Central

    Golshani, Maryam; Rafati, Sima; Jahanian-Najafabadi, Ali; Nejati-Moheimani, Mehdi; Siadat, Seyed Davar; Shahcheraghi, Fereshteh; Bouzari, Saeid

    2015-01-01

    Globally, Brucella melitensis and B. abortus are the most common cause of human brucellosis. The outer membrane protein 31 (Omp31) and L7/L12 are immunodominant and protective antigens conserved in human Brucella pathogens which are considered as potential vaccine candidates. We aimed to design the fusion protein from Brucella L7/L12 and truncated Omp31proteins, in silico, clone the fusion in pET28a vector, and express it in Escherichia coli host. Two possible fusion forms, L7/L12-TOmp31 and TOmp31-L7/L12 were subjected to in silico modeling and analysis. Analysis and validation of the fusion proteins with three dimensional (3D) models showed that both models are in the range of native proteins. However, L7/L12-Tomp31 structure was more valid than the TOmp31-L7/L12 model and subjected to in vitro production. The major histocompatibility complex (MHC II) epitope mapping using IEDB database indicated that the model contained good MHC II binders. The L7/L12-TOmp31 coding sequence was cloned in pET28a vector. The integrity of the construct was confirmed by polymerase chain reaction, restriction enzyme mapping, and sequencing. The fusion was successfully expressed in E. coli BL21 (DE3) by induction with isopropyl β-D-thiogalactopyranoside. The rL7/L12-TOmp31 was purified with Ni-NTA column. The yield of the purified rL7/L12-TOmp31 was estimated by Bradford method and found to be 40 mg/L of the culture. Western blotting with anti-His antibody revealed a specific reactivity with purified rL7/L12-TOmp31 produced in E. coli and showed the functional expression in the prokaryotic system. In this study, a new protein vaccine candidate against brucellosis was constructed with the help of bioinformatics tools and the construct was expressed in the bacterial host. Studies evaluating the immunogenicity and cross-protection of this fusion protein against B. melitensis and B. abortus are underway. PMID:26752992

  3. Transformation of tamoxifen and its major metabolites during water chlorination: Identification and in silico toxicity assessment of their disinfection byproducts.

    PubMed

    Negreira, Noelia; Regueiro, Jorge; López de Alda, Miren; Barceló, Damià

    2015-11-15

    The selective estrogen receptor modulator tamoxifen is the most commonly used drug for the treatment and prevention of breast cancer. Tamoxifen is considered as a pro-drug since it is known to exert its pharmacological effect through its major active metabolites, 4-hydroxy-tamoxifen and 4-hydroxy-N-desmethyl-tamoxifen, which are mainly excreted in the urine in the days following administration. In the present work, the reactivity of tamoxifen and its major active metabolites in free chlorine-containing water was investigated for the first time. Under the studied chlorination conditions, tamoxifen was fairly stable whereas its metabolites were quickly degraded. A total of thirteen chlorinated byproducts were tentatively identified by ultra-high performance liquid chromatography coupled to high-resolution hybrid quadrupole-Orbitrap tandem mass spectrometry. Time-course profiles of the identified byproducts were followed in real wastewater samples under conditions that simulate wastewater disinfection. A preliminary assessment of their acute aquatic toxicity at two trophic levels by means of quantitative structure-activity relationship models showed that the identified byproducts were up to 110-fold more toxic than the parent compounds. PMID:26320721

  4. Proposal of an in silico profiler for categorisation of repeat dose toxicity data of hair dyes.

    PubMed

    Nelms, M D; Ates, G; Madden, J C; Vinken, M; Cronin, M T D; Rogiers, V; Enoch, S J

    2015-05-01

    This study outlines the analysis of 94 chemicals with repeat dose toxicity data taken from Scientific Committee on Consumer Safety opinions for commonly used hair dyes in the European Union. Structural similarity was applied to group these chemicals into categories. Subsequent mechanistic analysis suggested that toxicity to mitochondria is potentially a key driver of repeat dose toxicity for chemicals within each of the categories. The mechanistic hypothesis allowed for an in silico profiler consisting of four mechanism-based structural alerts to be proposed. These structural alerts related to a number of important chemical classes such as quinones, anthraquinones, substituted nitrobenzenes and aromatic azos. This in silico profiler is intended for grouping chemicals into mechanism-based categories within the adverse outcome pathway paradigm. PMID:24888375

  5. Porcine myofibrillar proteins as potential precursors of bioactive peptides - an in silico study.

    PubMed

    Kęska, Paulina; Stadnik, Joanna

    2016-06-15

    Selected porcine myofibrillar proteins have been assessed as potential precursors of bioactive peptides based on in silico analysis. The potential of protein sequences for releasing peptides was evaluated by determining the profile of their potential biological activity and the frequency of occurrence of fragments with a given activity using the BIOPEP database. Digestive enzymes: pepsin, trypsin and chymotrypsin have been used for the in silico proteolysis with the use of the "Enzyme(s) action" tool in BIOPEP. After simulated gastrointestinal digestion the tested sequences of pig myofibrillar proteins are a potential source of a total of 399 peptides with activities such as enzyme inhibition, antioxidative, hypotensive, stimulating or regulating various body functions and antiamnestic activities. Within the intact proteins and after simulated gastrointestinal digestion, dipeptidyl peptidase IV inhibitory peptide sequences were the most frequently observed. The results indicate that pork myofibrillar proteins are a promising source of peptides with biological activity. PMID:27247979

  6. A Newton Cooperative Genetic Algorithm Method for In Silico Optimization of Metabolic Pathway Production

    PubMed Central

    Mohamad, Mohd Saberi; Abdullah, Afnizanfaizal

    2015-01-01

    This paper presents an in silico optimization method of metabolic pathway production. The metabolic pathway can be represented by a mathematical model known as the generalized mass action model, which leads to a complex nonlinear equations system. The optimization process becomes difficult when steady state and the constraints of the components in the metabolic pathway are involved. To deal with this situation, this paper presents an in silico optimization method, namely the Newton Cooperative Genetic Algorithm (NCGA). The NCGA used Newton method in dealing with the metabolic pathway, and then integrated genetic algorithm and cooperative co-evolutionary algorithm. The proposed method was experimentally applied on the benchmark metabolic pathways, and the results showed that the NCGA achieved better results compared to the existing methods. PMID:25961295

  7. In Silico Identification Software (ISIS): A Machine Learning Approach to Tandem Mass Spectral Identification of Lipids

    SciTech Connect

    Kangas, Lars J.; Metz, Thomas O.; Isaac, Georgis; Schrom, Brian T.; Ginovska-Pangovska, Bojana; Wang, Luning; Tan, Li; Lewis, Robert R.; Miller, John H.

    2012-05-15

    Liquid chromatography-mass spectrometry-based metabolomics has gained importance in the life sciences, yet it is not supported by software tools for high throughput identification of metabolites based on their fragmentation spectra. An algorithm (ISIS: in silico identification software) and its implementation are presented and show great promise in generating in silico spectra of lipids for the purpose of structural identification. Instead of using chemical reaction rate equations or rules-based fragmentation libraries, the algorithm uses machine learning to find accurate bond cleavage rates in a mass spectrometer employing collision-induced dissocia-tion tandem mass spectrometry. A preliminary test of the algorithm with 45 lipids from a subset of lipid classes shows both high sensitivity and specificity.

  8. Prioritization of in silico models and molecular descriptors for the assessment of ready biodegradability.

    PubMed

    Fernández, Alberto; Rallo, Robert; Giralt, Francesc

    2015-10-01

    Ready biodegradability is a key property for evaluating the long-term effects of chemicals on the environment and human health. As such, it is used as a screening test for the assessment of persistent, bioaccumulative and toxic substances. Regulators encourage the use of non-testing methods, such as in silico models, to save money and time. A dataset of 757 chemicals was collected to assess the performance of four freely available in silico models that predict ready biodegradability. They were applied to develop a new consensus method that prioritizes the use of each individual model according to its performance on chemical subsets driven by the presence or absence of different molecular descriptors. This consensus method was capable of almost eliminating unpredictable chemicals, while the performance of combined models was substantially improved with respect to that of the individual models. PMID:26160046

  9. In silico method for modelling metabolism and gene product expression at genome scale

    SciTech Connect

    Lerman, Joshua A.; Hyduke, Daniel R.; Latif, Haythem; Portnoy, Vasiliy A.; Lewis, Nathan E.; Orth, Jeffrey D.; Rutledge, Alexandra C.; Smith, Richard D.; Adkins, Joshua N.; Zengler, Karsten; Palsson, Bernard O.

    2012-07-03

    Transcription and translation use raw materials and energy generated metabolically to create the macromolecular machinery responsible for all cellular functions, including metabolism. A biochemically accurate model of molecular biology and metabolism will facilitate comprehensive and quantitative computations of an organism's molecular constitution as a function of genetic and environmental parameters. Here we formulate a model of metabolism and macromolecular expression. Prototyping it using the simple microorganism Thermotoga maritima, we show our model accurately simulates variations in cellular composition and gene expression. Moreover, through in silico comparative transcriptomics, the model allows the discovery of new regulons and improving the genome and transcription unit annotations. Our method presents a framework for investigating molecular biology and cellular physiology in silico and may allow quantitative interpretation of multi-omics data sets in the context of an integrated biochemical description of an organism.

  10. In silico method for modelling metabolism and gene product expression at genome scale

    PubMed Central

    Lerman, Joshua A.; Hyduke, Daniel R.; Latif, Haythem; Portnoy, Vasiliy A.; Lewis, nathan E.; Orth, Jeffrey D.; Schrimpe-Rutledge, Alexandra C.; Smith, Richard D.; Adkins, Joshua n.; Zengler, Karsten; Palsson, Bernhard O.

    2013-01-01

    Transcription and translation use raw materials and energy generated metabolically to create the macromolecular machinery responsible for all cellular functions, including metabolism. A biochemically accurate model of molecular biology and metabolism will facilitate comprehensive and quantitative computations of an organism's molecular constitution as a function of genetic and environmental parameters. Here we formulate a model of metabolism and macromolecular expression. Prototyping it using the simple microorganism Thermotoga maritima, we show our model accurately simulates variations in cellular composition and gene expression. Moreover, through in silico comparative transcriptomics, the model allows the discovery of new regulons and improving the genome and transcription unit annotations. Our method presents a framework for investigating molecular biology and cellular physiology in silico and may allow quantitative interpretation of multi-omics data sets in the context of an integrated biochemical description of an organism. PMID:22760628

  11. Cellular modeling of cancer invasion: Integration of in silico and in vitro approaches

    PubMed Central

    Kam, Yoonseok; Rejniak, Katarzyna A.; Anderson, Alexander R.A.

    2011-01-01

    Cancer invasion is one of the hallmarks of cancer and a prerequisite for cancer metastasis. However, the invasive process is very complex, depending on multiple correlated intrinsic and environmental factors, and thus is difficult to study experimentally in a fully controlled way. Therefore, there is an increased demand for interdisciplinary integrated approaches combining laboratory experiments with multiscale in silico modeling. In this review, we will summarize current computational techniques applicable to model cancer invasion in silico, with a special focus on a class of individual-cell-based models developed in our laboratories. We also discuss their integration with traditional and novel in vitro experimentation, including new invasion assays whose design was inspired by computational modeling. PMID:21465465

  12. Application of in silico modelling to estimate toxicity of migrating substances from food packaging.

    PubMed

    Price, Nicholas; Chaudhry, Qasim

    2014-09-01

    This study derived toxicity estimates for a set of 136 chemical migrants from food packaging materials using in silico (computational) modelling and read across approaches. Where available, the predicted results for mutagenicity and carcinogenicity were compared with published experimental data. As the packaging compounds are subject to safety assessment, the migrating substances were more likely to be negative for both the endpoints. A set of structural analogues with positive experimental data for carcinogenicity and/or mutagenicity was therefore used as a positive comparator. The results showed that a weight of evidence assembled from different in silico models and read-across from already-tested structurally similar compounds can provide a rapid and reliable means for rapid screening of new yet-untested intentional or unintentional chemical compounds that may migrate to packaged foodstuffs. PMID:24923263

  13. Identification of Xenoestrogens in Food Additives by an Integrated in Silico and in Vitro Approach

    PubMed Central

    Amadasi, Alessio; Mozzarelli, Andrea; Meda, Clara; Maggi, Adriana; Cozzini, Pietro

    2009-01-01

    In the search for xenoestrogens within food additives, we have analyzed the Joint FAO-WHO expert committee database, containing 1500 compounds, using an integrated in silico and in vitro approach. This analysis identified 31 potential estrogen receptor α ligands that were reduced to 13 upon applying a stringent filter based on ligand volume and binding mode. Among the 13 potential xenoestrogens, four were already known to exhibit an estrogenic activity, and the other nine were assayed in vitro, determining the binding affinity to the receptor and biological effects. Propyl gallate was found to act as an antagonist, and 4-hexylresorcinol was found to act as a potent transactivator; both ligands were active at nanomolar concentrations, as predicted by the in silico analysis. Some caution should be issued for the use of propyl gallate and 4-hexylresorcinol as food additives. PMID:19063592

  14. Assessing the environmental fate of S-metolachlor, its commercial product Mercantor Gold® and their photoproducts using a water-sediment test and in silico methods.

    PubMed

    Gutowski, Lukasz; Baginska, Ewelina; Olsson, Oliver; Leder, Christoph; Kümmerer, Klaus

    2015-11-01

    Pesticides enter surface and groundwater by several routes in which partition to sediment contributes to their fate by abiotic (e.g. photolysis, hydrolysis) and biotic processes. Yet, little is known about S-metolachlor (SM) transformation in water-sediment systems. Therefore, a newly developed screening water-sediment test (WST) was applied to compare biodegradation and sorption processes between pure SM and Mercantor Gold® (MG), a commercial formulation of SM. Photolysis in water was performed by Xe lamp irradiation. Subsequently, the biodegradability of SM and MG photolysis mixtures was examined in WST. The primary elimination of SM from water phase was monitored and structures of its TPs resulting from biotransformation (bio-TPs) were elucidated by LC-MS/MS. SM was extracted from sediment in order to estimate the role of sorption in WST for its elimination. A set of in silico prediction software tools was applied for toxicity assessment of SM and its bio-TPs. Obtained results suggest that the MG adjuvants do not significantly affect biodegradation, but do influence diffusion of SM into sediment. 50% of SM could not be re-extracted from sediment with 0.01 M CaCl2 aqueous solution recommended in OECD test guideline for adsorption. Neither the parent compound nor the photo-TPs were biodegraded. However, new bio-TPs have been generated from SM and MG photo-TPs due to bacterial activity in the water-sediment interphase. Moreover, according to in silico assessment of the bio-TPs the biotransformation might lead to an increased toxicity to the water organisms compared with the SM. This might raise concerns of bio-TPs presence in the environment. PMID:26299980

  15. In silico enzymatic synthesis of a 400,000 compound biochemical database for nontargeted metabolomics.

    PubMed

    Menikarachchi, Lochana C; Hill, Dennis W; Hamdalla, Mai A; Mandoiu, Ion I; Grant, David F

    2013-09-23

    Current methods of structure identification in mass-spectrometry-based nontargeted metabolomics rely on matching experimentally determined features of an unknown compound to those of candidate compounds contained in biochemical databases. A major limitation of this approach is the relatively small number of compounds currently included in these databases. If the correct structure is not present in a database, it cannot be identified, and if it cannot be identified, it cannot be included in a database. Thus, there is an urgent need to augment metabolomics databases with rationally designed biochemical structures using alternative means. Here we present the In Vivo/In Silico Metabolites Database (IIMDB), a database of in silico enzymatically synthesized metabolites, to partially address this problem. The database, which is available at http://metabolomics.pharm.uconn.edu/iimdb/, includes ~23,000 known compounds (mammalian metabolites, drugs, secondary plant metabolites, and glycerophospholipids) collected from existing biochemical databases plus more than 400,000 computationally generated human phase-I and phase-II metabolites of these known compounds. IIMDB features a user-friendly web interface and a programmer-friendly RESTful web service. Ninety-five percent of the computationally generated metabolites in IIMDB were not found in any existing database. However, 21,640 were identical to compounds already listed in PubChem, HMDB, KEGG, or HumanCyc. Furthermore, the vast majority of these in silico metabolites were scored as biological using BioSM, a software program that identifies biochemical structures in chemical structure space. These results suggest that in silico biochemical synthesis represents a viable approach for significantly augmenting biochemical databases for nontargeted metabolomics applications. PMID:23991755

  16. Divergent Metabolic Phenotype between Two Sisters with Congenital Generalized Lipodystrophy Due to Double AGPAT2 Homozygous Mutations. A Clinical, Genetic and In Silico Study

    PubMed Central

    Cortés, Víctor A.; Smalley, Susan V.; Goldenberg, Denisse; Lagos, Carlos F.; Hodgson, María I.; Santos, José L.

    2014-01-01

    Congenital generalized lipodystrophy (CGL) is a rare autosomal recessive disorder characterized by extreme reduction of white adipose tissue (WAT) mass. CGL type 1 is the most frequent form and is caused by mutations in AGPAT2. Genetic and clinical studies were performed in two affected sisters of a Chilean family. These patients have notoriously dissimilar metabolic abnormalities that correlate with differential levels of circulating leptin and soluble leptin receptor fraction. Sequencing of AGPAT2 exons and exon-intron boundaries revealed two homozygous mutations in both sisters. Missense mutation c.299G>A changes a conserved serine in the acyltransferase NHX4D motif of AGPAT2 (p.Ser100Asn). Intronic c.493-1G>C mutation destroy a conserved splicing site that likely leads to exon 4 skipping and deletion of whole AGPAT2 substrate binding domain. In silico protein modeling provided insights of the mechanisms of lack of catalytic activity owing to both mutations. PMID:24498038

  17. Human thromboxane A2 receptor genetic variants: in silico, in vitro and "in platelet" analysis.

    PubMed

    Gleim, Scott; Stitham, Jeremiah; Tang, Wai Ho; Li, Hong; Douville, Karen; Chelikani, Prashen; Rade, Jeffrey J; Martin, Kathleen A; Hwa, John

    2013-01-01

    Thromboxane and its receptor have emerged as key players in modulating vascular thrombotic events. Thus, a dysfunctional hTP genetic variant may protect against (hypoactivity) or promote (hyperactivity) vascular events, based upon its activity on platelets. After extensive in silico analysis, six hTP-α variants were selected (C(68)S, V(80)E, E(94)V, A(160)T, V(176)E, and V(217)I) for detailed biochemical studies based on structural proximity to key regions involved in receptor function and in silico predictions. Variant biochemical profiles ranged from severe instability (C(68)S) to normal (V(217)I), with most variants demonstrating functional alteration in binding, expression or activation (V(80)E, E(94)V, A(160)T, and V(176)E). In the absence of patient platelet samples, we developed and validated a novel megakaryocyte based system to evaluate human platelet function in the presence of detected dysfunctional genetic variants. Interestingly, variant V80E exhibited reduced platelet activation whereas A160T demonstrated platelet hyperactivity. This report provides the most comprehensive in silico, in vitro and "in platelet" evaluation of hTP variants to date and highlightscurrent inherent problems in evaluating genetic variants, with possible solutions. The study additionally provides clinical relevance to characterized dysfunctional hTP variants. PMID:23840660

  18. Trypanothione Reductase: A Target Protein for a Combined In Vitro and In Silico Screening Approach

    PubMed Central

    Garoff, Linnéa; Noack, Sandra; Krauth-Siegel, R. Luise; Selzer, Paul M.

    2015-01-01

    With the goal to identify novel trypanothione reductase (TR) inhibitors, we performed a combination of in vitro and in silico screening approaches. Starting from a highly diverse compound set of 2,816 compounds, 21 novel TR inhibiting compounds could be identified in the initial in vitro screening campaign against T. cruzi TR. All 21 in vitro hits were used in a subsequent similarity search-based in silico screening on a database containing 200,000 physically available compounds. The similarity search resulted in a data set containing 1,204 potential TR inhibitors, which was subjected to a second in vitro screening campaign leading to 61 additional active compounds. This corresponds to an approximately 10-fold enrichment compared to the initial pure in vitro screening. In total, 82 novel TR inhibitors with activities down to the nM range could be identified proving the validity of our combined in vitro/in silico approach. Moreover, the four most active compounds, showing IC50 values of <1 μM, were selected for determining the inhibitor constant. In first on parasites assays, three compounds inhibited the proliferation of bloodstream T. brucei cell line 449 with EC50 values down to 2 μM. PMID:26042772

  19. In silico identification of anthropogenic chemicals as ligands of zebrafish sex hormone binding globulin

    SciTech Connect

    Thorsteinson, Nels; Ban, Fuqiang; Santos-Filho, Osvaldo; Tabaei, Seyed M.H.; Miguel-Queralt, Solange; Underhill, Caroline; Cherkasov, Artem Hammond, Geoffrey L.

    2009-01-01

    Anthropogenic compounds with the capacity to interact with the steroid-binding site of sex hormone binding globulin (SHBG) pose health risks to humans and other vertebrates including fish. Building on studies of human SHBG, we have applied in silico drug discovery methods to identify potential binders for SHBG in zebrafish (Danio rerio) as a model aquatic organism. Computational methods, including; homology modeling, molecular dynamics simulations, virtual screening, and 3D QSAR analysis, successfully identified 6 non-steroidal substances from the ZINC chemical database that bind to zebrafish SHBG (zfSHBG) with low-micromolar to nanomolar affinities, as determined by a competitive ligand-binding assay. We also screened 80,000 commercial substances listed by the European Chemicals Bureau and Environment Canada, and 6 non-steroidal hits from this in silico screen were tested experimentally for zfSHBG binding. All 6 of these compounds displaced the [{sup 3}H]5{alpha}-dihydrotestosterone used as labeled ligand in the zfSHBG screening assay when tested at a 33 {mu}M concentration, and 3 of them (hexestrol, 4-tert-octylcatechol, and dihydrobenzo(a)pyren-7(8H)-one) bind to zfSHBG in the micromolar range. The study demonstrates the feasibility of large-scale in silico screening of anthropogenic compounds that may disrupt or highjack functionally important protein:ligand interactions. Such studies could increase the awareness of hazards posed by existing commercial chemicals at relatively low cost.

  20. Microbial interaction networks in soil and in silico

    NASA Astrophysics Data System (ADS)

    Vetsigian, Kalin

    2012-02-01

    Soil harbors a huge number of microbial species interacting through secretion of antibiotics and other chemicals. What patterns of species interactions allow for this astonishing biodiversity to be sustained, and how do these interactions evolve? I used a combined experimental-theoretical approach to tackle these questions. Focusing on bacteria from the genus Steptomyces, known for their diverse secondary metabolism, I isolated 64 natural strains from several individual grains of soil and systematically measured all pairwise interactions among them. Quantitative measurements on such scale were enabled by a novel experimental platform based on robotic handling, a custom scanner array and automatic image analysis. This unique platform allowed the simultaneous capturing of ˜15,000 time-lapse movies of growing colonies of each isolate on media conditioned by each of the other isolates. The data revealed a rich network of strong negative (inhibitory) and positive (stimulating) interactions. Analysis of this network and the phylogeny of the isolates, together with mathematical modeling of microbial communities, revealed that: 1) The network of interactions has three special properties: ``balance'', ``bi- modality'' and ``reciprocity''; 2) The interaction network is fast evolving; 3) Mathematical modeling explains how rapid evolution can give rise to the three special properties through an interplay between ecology and evolution. These properties are not a result of stable co-existence, but rather of continuous evolutionary turnover of strains with different production and resistance capabilities.

  1. Comparative Genomic Analysis of Drechmeria coniospora Reveals Core and Specific Genetic Requirements for Fungal Endoparasitism of Nematodes

    PubMed Central

    Thakur, Nishant; Arguel, Marie-Jeanne; Polanowska, Jolanta; Henrissat, Bernard; Record, Eric; Magdelenat, Ghislaine; Barbe, Valérie; Raffaele, Sylvain; Barbry, Pascal

    2016-01-01

    Drechmeria coniospora is an obligate fungal pathogen that infects nematodes via the adhesion of specialized spores to the host cuticle. D. coniospora is frequently found associated with Caenorhabditis elegans in environmental samples. It is used in the study of the nematode’s response to fungal infection. Full understanding of this bi-partite interaction requires knowledge of the pathogen’s genome, analysis of its gene expression program and a capacity for genetic engineering. The acquisition of all three is reported here. A phylogenetic analysis placed D. coniospora close to the truffle parasite Tolypocladium ophioglossoides, and Hirsutella minnesotensis, another nematophagous fungus. Ascomycete nematopathogenicity is polyphyletic; D. coniospora represents a branch that has not been molecularly characterized. A detailed in silico functional analysis, comparing D. coniospora to 11 fungal species, revealed genes and gene families potentially involved in virulence and showed it to be a highly specialized pathogen. A targeted comparison with nematophagous fungi highlighted D. coniospora-specific genes and a core set of genes associated with nematode parasitism. A comparative gene expression analysis of samples from fungal spores and mycelia, and infected C. elegans, gave a molecular view of the different stages of the D. coniospora lifecycle. Transformation of D. coniospora allowed targeted gene knock-out and the production of fungus that expresses fluorescent reporter genes. It also permitted the initial characterisation of a potential fungal counter-defensive strategy, involving interference with a host antimicrobial mechanism. This high-quality annotated genome for D. coniospora gives insights into the evolution and virulence of nematode-destroying fungi. Coupled with genetic transformation, it opens the way for molecular dissection of D. coniospora physiology, and will allow both sides of the interaction between D. coniospora and C. elegans, as well as the

  2. Comparative Genomic Analysis of Drechmeria coniospora Reveals Core and Specific Genetic Requirements for Fungal Endoparasitism of Nematodes.

    PubMed

    Lebrigand, Kevin; He, Le D; Thakur, Nishant; Arguel, Marie-Jeanne; Polanowska, Jolanta; Henrissat, Bernard; Record, Eric; Magdelenat, Ghislaine; Barbe, Valérie; Raffaele, Sylvain; Barbry, Pascal; Ewbank, Jonathan J

    2016-05-01

    Drechmeria coniospora is an obligate fungal pathogen that infects nematodes via the adhesion of specialized spores to the host cuticle. D. coniospora is frequently found associated with Caenorhabditis elegans in environmental samples. It is used in the study of the nematode's response to fungal infection. Full understanding of this bi-partite interaction requires knowledge of the pathogen's genome, analysis of its gene expression program and a capacity for genetic engineering. The acquisition of all three is reported here. A phylogenetic analysis placed D. coniospora close to the truffle parasite Tolypocladium ophioglossoides, and Hirsutella minnesotensis, another nematophagous fungus. Ascomycete nematopathogenicity is polyphyletic; D. coniospora represents a branch that has not been molecularly characterized. A detailed in silico functional analysis, comparing D. coniospora to 11 fungal species, revealed genes and gene families potentially involved in virulence and showed it to be a highly specialized pathogen. A targeted comparison with nematophagous fungi highlighted D. coniospora-specific genes and a core set of genes associated with nematode parasitism. A comparative gene expression analysis of samples from fungal spores and mycelia, and infected C. elegans, gave a molecular view of the different stages of the D. coniospora lifecycle. Transformation of D. coniospora allowed targeted gene knock-out and the production of fungus that expresses fluorescent reporter genes. It also permitted the initial characterisation of a potential fungal counter-defensive strategy, involving interference with a host antimicrobial mechanism. This high-quality annotated genome for D. coniospora gives insights into the evolution and virulence of nematode-destroying fungi. Coupled with genetic transformation, it opens the way for molecular dissection of D. coniospora physiology, and will allow both sides of the interaction between D. coniospora and C. elegans, as well as the

  3. Inclusion complex of erlotinib with sulfobutyl ether-β-cyclodextrin: Preparation, characterization, in silico, in vitro and in vivo evaluation.

    PubMed

    Devasari, Naresh; Dora, Chander Parkash; Singh, Charan; Paidi, Sharan Reddy; Kumar, Vivek; Sobhia, Masilamani Elizabeth; Suresh, Sarasija

    2015-12-10

    The aim of the study was to investigate the impact of erlotinib sulfobutyl ether beta-cyclodextrin complex (ERL-SBE-β-CD) on ERL dissolution rate and oral bioavailability. Preliminary comparative phase solubility study indicated ERL exhibited maximum solubility in SBE-β-CD solution. Optimal experimental design confirmed freeze drying of SBE-β-CD:ERL in 1:1.05 molar ratio as the optimum method. Differential scanning calorimetry (DSC), Fourier transformation infrared spectroscopy (FT-IR), powder X-ray diffractometry (PXRD), proton nuclear magnetic resonance ((1)H NMR) and two-dimensional rotating-frame Overhauser effect spectroscopy (2D ROESY NMR) confirmed the inclusion complexation. The in silico computational study, employed to analyze the comparative interactions of ERL with SBE-β-CD and β-CD, indicated ease of ERL-SBE-β-CD complexation. In vitro dissolution and in vivo bioavailability studies further confirmed the ERL-SBE-β-CD as a valuable approach to enhance ERL oral bioavailability with 3.6-fold increase in relative oral bioavailability with higher Cmax (134.29 ± 36.51 vs. 42.36 ± 1.75 μg/ml) and AUC0-∞ (2103.47 ± 156.75 vs.580.43 ± 71.91 μg/ml h) over the free drug. The complex exhibited 3.2-fold increase in Cmax with 5.4-fold decrease in Tmax (0.5 ± 0.2 vs. 2.7 ± 0.8h) in comparison to pure ERL. Thus, ERL-SBE-β-CD complexation exhibits a potential to enhance oral bioavailability of ERL leading to reduce dose and dose-related side effects. PMID:26428157

  4. Quantum mechanical approaches to in silico enzyme characterization and drug design

    SciTech Connect

    Nilmeier, J P; Fattebert, J L; Jacobson, M P; Kalyanaraman, C

    2012-01-17

    The astonishing, exponentially increasing rates of genome sequencing has led to one of the most significant challenges for the biological and computational sciences in the 21st century: assigning the likely functions of the encoded proteins. Enzymes represent a particular challenge, and a critical one, because the universe of enzymes is likely to contain many novel functions that may be useful for synthetic biology, or as drug targets. Current approaches to protein annotation are largely based on bioinformatics. At the simplest level, this annotation involves transferring the annotations of characterized enzymes to related sequences. In practice, however, there is no simple, sequence based criterion for transferring annotations, and bioinformatics alone cannot propose new enzymatic functions. Structure-based computational methods have the potential to address these limitations, by identifying potential substrates of enzymes, as we and others have shown. One successful approach has used in silico 'docking' methods, more commonly applied in structure-based drug design, to identify possible metabolite substrates. A major limitation of this approach is that it only considers substrate binding, and does not directly assess the potential of the enzyme to catalyze a particular reaction using a particular substrate. That is, substrate binding affinity is necessary but not sufficient to assign function. A reaction profile is ultimately what is needed for a more complete quantitative description of function. To address this rather fundamental limitation, they propose to use quantum mechanical methods to explicitly compute transition state barriers that govern the rates of catalysis. Although quantum mechanical, and mixed quantum/classical (QM/MM), methods have been used extensively to investigate enzymatic reactions, the focus has been primarily on elucidating complex reaction mechanisms. Here, the key catalytic steps are known, and they use these methods quantify substrate

  5. Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis.

    PubMed

    Hanchate, Naresh K; Kondoh, Kunio; Lu, Zhonghua; Kuang, Donghui; Ye, Xiaolan; Qiu, Xiaojie; Pachter, Lior; Trapnell, Cole; Buck, Linda B

    2015-12-01

    The sense of smell allows chemicals to be perceived as diverse scents. We used single-neuron RNA sequencing to explore the developmental mechanisms that shape this ability as nasal olfactory neurons mature in mice. Most mature neurons expressed only one of the ~1000 odorant receptor genes (Olfrs) available, and at a high level. However, many immature neurons expressed low levels of multiple Olfrs. Coexpressed Olfrs localized to overlapping zones of the nasal epithelium, suggesting regional biases, but not to single genomic loci. A single immature neuron could express Olfrs from up to seven different chromosomes. The mature state in which expression of Olfr genes is restricted to one per neuron emerges over a developmental progression that appears to be independent of neuronal activity involving sensory transduction molecules. PMID:26541607

  6. In-silico analysis of Aspergillus niger beta-glucosidases

    NASA Astrophysics Data System (ADS)

    Yeo S., L.; Shazilah, K.; Suhaila, S.; Abu Bakar F., D.; Murad A. M., A.

    2014-09-01

    Genomic data mining was carried out and revealed a total of seventeen β-glucosidases in filamentous fungi Aspergillus niger. Two of them belonged to glycoside hydrolase family 1 (GH1) while the rest belonged to genes in family 3 (GH3). These proteins were then named according to the nomenclature as proposed by the International Union of Biochemistry (IUB), starting from the lowest pI and glycoside hydrolase family. Their properties were predicted using various bionformatic tools showing the presence of domains for signal peptide and active sites. Interestingly, one particular domain, PA14 (protective antigen) was present in four of the enzymes, predicted to be involved in carbohydrate binding. A phylogenetic tree grouped the two glycoside hydrolase families with GH1 and GH3 related organisms. This study showed that the various domains present in these β-glucosidases are postulated to be crucial for the survival of this fungus, as supported by other analysis.

  7. In silico prediction of drug targets in Vibrio cholerae.

    PubMed

    Katara, Pramod; Grover, Atul; Kuntal, Himani; Sharma, Vinay

    2011-10-01

    Identification of potential drug targets is the first step in the process of modern drug discovery, subjected to their validation and drug development. Whole genome sequences of a number of organisms allow prediction of potential drug targets using sequence comparison approaches. Here, we present a subtractive approach exploiting the knowledge of global gene expression along with sequence comparisons to predict the potential drug targets more efficiently. Based on the knowledge of 155 known virulence and their coexpressed genes mined from microarray database in the public domain, 357 coexpressed probable virulence genes for Vibrio cholerae were predicted. Based on screening of Database of Essential Genes using blastn, a total of 102 genes out of these 357 were enlisted as vitally essential genes, and hence good putative drug targets. As the effective drug target is a protein which is only present in the pathogen, similarity search of these 102 essential genes against human genome sequence led to subtraction of 66 genes, thus leaving behind a subset of 36 genes whose products have been called as potential drug targets. The gene ontology analysis using Blast2GO of these 36 genes revealed their roles in important metabolic pathways of V. cholerae or on the surface of the pathogen. Thus, we propose that the products of these genes be evaluated as target sites of drugs against V. cholerae in future investigations. PMID:21174131

  8. In silico experimental evolution: a tool to test evolutionary scenarios.

    PubMed

    Batut, Bérénice; Parsons, David P; Fischer, Stephan; Beslon, Guillaume; Knibbe, Carole

    2013-01-01

    Comparative genomics has revealed that some species have exceptional genomes, compared to their closest relatives. For instance, some species have undergone a strong reduction of their genome with a drastic reduction of their genic repertoire. Deciphering the causes of these atypical trajectories can be very difficult because of the many phenomena that are intertwined during their evolution (e.g. changes of population size, environment structure and dynamics, selection strength, mutation rates...). Here we propose a methodology based on synthetic experiments to test the individual effect of these phenomena on a population of simulated organisms. We developed an evolutionary model--aevol--in which evolutionary conditions can be changed one at a time to test their effects on genome size and organization (e.g. coding ratio). To illustrate the proposed approach, we used aevol to test the effects of a strong reduction in the selection strength on a population of (simulated) bacteria. Our results show that this reduction of selection strength leads to a genome reduction of ~35% with a slight loss of coding sequences (~15% of the genes are lost--mainly those for which the contribution to fitness is the lowest). More surprisingly, under a low selection strength, genomes undergo a strong reduction of the noncoding compartment (~55% of the noncoding sequences being lost). These results are consistent with what is observed in reduced Prochlorococcus strains (marine cyanobacteria) when compared to close relatives. PMID:24564457

  9. In silico characterization of hypothetical proteins from Paracoccidioides lutzii.

    PubMed

    Silva, P F F; Novaes, E; Pereira, M; Soares, C M A; Borges, C L; Salem-Izacc, S M

    2015-01-01

    Nearly 60% of Paracoccidioides lutzii genes encode products annotated as hypothetical or predicted proteins (HPs). In this study, we describe the global detection and functional inference of HPs, using computational methods based on sequence similarity, identification of targeting signals, presence of known protein domains, and use of the Gene Ontology functional classification scheme. Our analysis enabled a high-throughput characterization of predicted cellular localization and presence of protein domains, clustering HPs into different functional categories including metabolism, localization, cell cycle, response to stimulus, and signaling. To investigate P. lutzii HP expression profiles, we used data obtained from the expressed sequence tag database (dbEST). These analyses revealed 2364 HPs expressed in different situations, namely in mycelial and yeast forms, during the transition from mycelium to yeast, and under conditions mimicking infection. Based on this transcriptomic data, we performed a functional enrichment analysis according to the domains present in the HPs expressed in each condition. The most overrepresented functional domains were those involved in the regulation of gene expression, suggesting important and as yet undescribed roles for these HPs in the adaptation of P. lutzii to environmental conditions. In addition, the expression profiles of six randomly selected HPs were analyzed by quantitative real-time polymerase chain reaction in order to verify their expression in the complementary DNA libraries analyzed in this investigation. The approach used in this study should improve functional characterization of P. lutzii HPs. PMID:26782383

  10. Transforming the Way We Teach Function Transformations

    ERIC Educational Resources Information Center

    Faulkenberry, Eileen Durand; Faulkenberry, Thomas J.

    2010-01-01

    In this article, the authors discuss "function," a well-defined rule that relates inputs to outputs. They have found that by using the input-output definition of "function," they can examine transformations of functions simply by looking at changes to input or output and the respective changes to the graph. Applying transformations to the input…

  11. Pharmacokinetics, brain distribution and plasma protein binding of carbamazepine and nine derivatives: new set of data for predictive in silico ADME models.

    PubMed

    Fortuna, Ana; Alves, Gilberto; Soares-da-Silva, Patrício; Falcão, Amílcar

    2013-11-01

    In silico approaches to predict absorption, distribution, metabolism and excretion (ADME) of new drug candidates are gaining a relevant importance in drug discovery programmes. When considering particularly the pharmacokinetics during the development of oral antiepileptic drugs (AEDs), one of the most prominent goals is designing compounds with good bioavailability and brain penetration. Thus, it is expected that in silico models able to predict these features may be applied during the early stages of AEDs discovery. The present investigation was mainly carried out in order to generate in vivo pharmacokinetic data that can be utilized for development and validation of in silico models. For this purpose, a single dose of each compound (1.4mmol/kg) was orally administered to male CD-1 mice. After quantifying the parent compound and main metabolites in plasma and brain up to 12h post-dosing, a non-compartmental pharmacokinetic analysis was performed and the corresponding brain/plasma ratios were calculated. Moreover the plasma protein binding was estimated in vitro applying the ultrafiltration procedure. The present in vivo pharmacokinetic characterization of the test compounds and corresponding metabolites demonstrated that the metabolism extensively compromised the in vivo activity of CBZ derivatives and their toxicity. Furthermore, it was clearly evidenced that the time to reach maximum peak concentration, bioavailability (given by the area under the curve) and metabolic stability (given by the AUC0-12h ratio of the parent compound and total systemic drug) influenced the in vivo pharmacological activities and must be considered as primary parameters to be investigated. All the test compounds presented brain/plasma ratios lower than 1.0, suggesting that the blood-brain barrier restricts drug entry into the brain. In agreement with in vitro studies already performed within our research group, CBZ, CBZ-10,11-epoxide and oxcarbazepine exhibited the highest brain

  12. In silico study of amyloid -protein folding and oligomerization

    NASA Astrophysics Data System (ADS)

    Urbanc, B.; Cruz, L.; Yun, S.; Buldyrev, S. V.; Bitan, G.; Teplow, D. B.; Stanley, H. E.

    2004-12-01

    Experimental findings suggest that oligomeric forms of the amyloid protein (A) play a critical role in Alzheimer's disease. Thus, elucidating their structure and the mechanisms of their formation is critical for developing therapeutic agents. We use discrete molecular dynamics simulations and a four-bead protein model to study oligomerization of two predominant alloforms, A40 and A42, at the atomic level. The four-bead model incorporates backbone hydrogen-bond interactions and amino acid-specific interactions mediated through hydrophobic and hydrophilic elements of the side chains. During the simulations we observe monomer folding and aggregation of monomers into oligomers of variable sizes. A40 forms significantly more dimers than A42, whereas pentamers are significantly more abundant in A42 relative to A40. Structure analysis reveals a turn centered at Gly-37-Gly-38 that is present in a folded A42 monomer but not in a folded A40 monomer and is associated with the first contacts that form during monomer folding. Our results suggest that this turn plays an important role in A42 pentamer formation. A pentamers have a globular structure comprising hydrophobic residues within the pentamer's core and hydrophilic N-terminal residues at the surface of the pentamer. The N termini of A40 pentamers are more spatially restricted than A42 pentamers. A40 pentamers form a -strand structure involving Ala-2-Phe-4, which is absent in A42 pentamers. These structural differences imply a different degree of hydrophobic core exposure between pentamers of the two alloforms, with the hydrophobic core of the Aβ42 pentamer being more exposed and thus more prone to form larger oligomers.

  13. Nucleosome positioning and composition modulate in silico chromatin flexibility.

    PubMed

    Clauvelin, N; Lo, P; Kulaeva, O I; Nizovtseva, E V; Diaz-Montes, J; Zola, J; Parashar, M; Studitsky, V M; Olson, W K

    2015-02-18

    The dynamic organization of chromatin plays an essential role in the regulation of gene expression and in other fundamental cellular processes. The underlying physical basis of these activities lies in the sequential positioning, chemical composition, and intermolecular interactions of the nucleosomes-the familiar assemblies of ∼150 DNA base pairs and eight histone proteins-found on chromatin fibers. Here we introduce a mesoscale model of short nucleosomal arrays and a computational framework that make it possible to incorporate detailed structural features of DNA and histones in simulations of short chromatin constructs. We explore the effects of nucleosome positioning and the presence or absence of cationic N-terminal histone tails on the 'local' inter-nucleosomal interactions and the global deformations of the simulated chains. The correspondence between the predicted and observed effects of nucleosome composition and numbers on the long-range communication between the ends of designed nucleosome arrays lends credence to the model and to the molecular insights gleaned from the simulated structures. We also extract effective nucleosome-nucleosome potentials from the simulations and implement the potentials in a larger-scale computational treatment of regularly repeating chromatin fibers. Our results reveal a remarkable effect of nucleosome spacing on chromatin flexibility, with small changes in DNA linker length significantly altering the interactions of nucleosomes and the dimensions of the fiber as a whole. In addition, we find that these changes in nucleosome positioning influence the statistical properties of long chromatin constructs. That is, simulated chromatin fibers with the same number of nucleosomes exhibit polymeric behaviors ranging from Gaussian to worm-like, depending upon nucleosome spacing. These findings suggest that the physical and mechanical properties of chromatin can span a wide range of behaviors, depending on nucleosome positioning, and

  14. Nucleosome positioning and composition modulate in silico chromatin flexibility

    NASA Astrophysics Data System (ADS)

    Clauvelin, N.; Lo, P.; Kulaeva, O. I.; Nizovtseva, E. V.; Diaz-Montes, J.; Zola, J.; Parashar, M.; Studitsky, V. M.; Olson, W. K.

    2015-02-01

    The dynamic organization of chromatin plays an essential role in the regulation of gene expression and in other fundamental cellular processes. The underlying physical basis of these activities lies in the sequential positioning, chemical composition, and intermolecular interactions of the nucleosomes—the familiar assemblies of ˜150 DNA base pairs and eight histone proteins—found on chromatin fibers. Here we introduce a mesoscale model of short nucleosomal arrays and a computational framework that make it possible to incorporate detailed structural features of DNA and histones in simulations of short chromatin constructs. We explore the effects of nucleosome positioning and the presence or absence of cationic N-terminal histone tails on the ‘local’ inter-nucleosomal interactions and the global deformations of the simulated chains. The correspondence between the predicted and observed effects of nucleosome composition and numbers on the long-range communication between the ends of designed nucleosome arrays lends credence to the model and to the molecular insights gleaned from the simulated structures. We also extract effective nucleosome-nucleosome potentials from the simulations and implement the potentials in a larger-scale computational treatment of regularly repeating chromatin fibers. Our results reveal a remarkable effect of nucleosome spacing on chromatin flexibility, with small changes in DNA linker length significantly altering the interactions of nucleosomes and the dimensions of the fiber as a whole. In addition, we find that these changes in nucleosome positioning influence the statistical properties of long chromatin constructs. That is, simulated chromatin fibers with the same number of nucleosomes exhibit polymeric behaviors ranging from Gaussian to worm-like, depending upon nucleosome spacing. These findings suggest that the physical and mechanical properties of chromatin can span a wide range of behaviors, depending on nucleosome

  15. Traditional Chinese medicine application in HIV: an in silico study.

    PubMed

    Huang, Hung-Jin; Jian, Yi-Ru; Chen, Calvin Yu-Chian

    2014-01-01

    Viral infection by human immunodeficiency virus (HIV) requires integration of viral DNA with host DNA which involves the binding of HIV integrase (IN) with its co-factor lens epithelium-derived growth factor (LEDGF/p75). Since disrupted binding of IN with LEDGF/p75 inhibits proliferation of HIV, inhibition or denaturation of IN is a possible method for inhibiting HIV replication. D77 is a known drug with demonstrated inhibition against HIV by binding to IN. Herein, we utilized D77 as a control to screen for traditional Chinese medicine (TCM) compounds that exhibit similar atomic-level characteristics. 9-Hydroxy-(10E)-octadecenoic acid and Beauveriolide I were found to have higher Dock Scores to IN than D77 through virtual screening. Multiple linear regression (R2 = 0.9790) and support vector machine (R2 = 0.9114) models consistently predicted potential bioactivity of the TCM candidates against IN. The 40 ns molecular dynamics simulation showed that the TCM compounds fulfilled the drug-like criteria of forming stable complexes with IN. Atomic-level investigations revealed that 9-hydroxy-(10E)-octadecenoic acid bound to an important residue A:Lys173, and Beauveriolide I formed stable interactions with the core LEDGF binding site and with Asn256 of the IN binding site on LEDGF. The TCM candidates also initiated loss of α-helices that could affect the functionality of IN. Taken together, the ability of 9-hydroxy-(10E)-octadecenoic acid and Beauveriolide I to (1) form stable interactions affecting IN-LEDGF binding and (2) have predicted bioactivity against IN suggests that the TCM candidates might be potential starting structures for developing compounds that may disrupt IN-LEDGF binding. An animated interactive 3D complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:40. PMID:23252879

  16. Symplectic wavelet transformation.

    PubMed

    Fan, Hong-Yi; Lu, Hai-Liang

    2006-12-01

    Usually a wavelet transform is based on dilated-translated wavelets. We propose a symplectic-transformed-translated wavelet family psi(*)(r,s)(z-kappa) (r,s are the symplectic transform parameters, |s|(2)-|r|(2)=1, kappa is a translation parameter) generated from the mother wavelet psi and the corresponding wavelet transformation W(psi)f(r,s;kappa)=integral(infinity)(-infinity)(d(2)z/pi)f(z)psi(*)(r,s)(z-kappa). This new transform possesses well-behaved properties and is related to the optical Fresnel transform in quantum mechanical version. PMID:17099740

  17. In silico analysis of Mn transporters (NRAMP1) in various plant species.

    PubMed

    Vatansever, Recep; Filiz, Ertugrul; Ozyigit, Ibrahim Ilker

    2016-03-01

    Manganese (Mn) is an essential micronutrient in plant life cycle. It may be involved in photosynthesis, carbohydrate and lipid biosynthesis, and oxidative stress protection. Mn deficiency inhibits the plant growth and development, and causes the various plant symptoms such as interveinal chlorosis and tissue necrosis. Despite its importance in plant life cycle, we still have limited knowledge about Mn transporters in many plant species. Therefore, this study aimed to identify and characterize high affinity Arabidopsis Mn root transporter NRAMP1 orthologs in 17 different plant species. Various in silico methods and digital gene expression data were used in identification and characterization of NRAMP1 homologs; physico-chemical properties of sequences were calculated, putative transmembrane domains (TMDs) and conserved motif signatures were determined, phylogenetic tree was constructed, 3D models and interactome map were generated, and gene expression data was analyzed. 49 NRAMP1 homologs were identified from proteome datasets of 17 plant species using AtNRAMP1 as query. Identified sequences were characterized with a NRAMP domain structure, 10-12 putative TMDs with cytosolic N- and C-terminuses, and 10-14 exons encoding a protein of 500-588 amino acids and 53.8-64.3 kDa molecular weight with basic characteristics. Consensus transport residues, GQSSTITGTYAGQY(/F)V(/I)MQGFLD(/E/N) between TMD-8 and 9 were identified in all sequences but putative N-linked glycosylation sites were not highly conserved. In phylogeny, NRAMP1 sequences demonstrated divergence in lower and higher plants as well as in monocots and dicots. Despite divergence of lower plant Physcomitrella patens in phylogeny, it showed similarity in superposed 3D models. Phylogenetic distribution of AtNRAMP1 and 6 homologs inferred a functional relationship to NRAMP6 sequences in Mn transport, while distribution of OsNRAMP1 and 5 homologs implicated an involvement of NRAMP1 sequences in Mn transport or a cross

  18. Discordance between in silico & in vitro analyses of ACE inhibitory & antioxidative peptides from mixed milk tryptic whey protein hydrolysate.

    PubMed

    Chatterjee, Alok; Kanawjia, S K; Khetra, Yogesh; Saini, Prerna

    2015-09-01

    ACE inhibitory and antioxidative peptides identified by LCMS/MS, from mixed milk (Bubalus bubalis and Bos taurus) tryptic whey protein hydrolysate, were compared with the in silico predictions. α la and ß lg sequences, both from Bubalus bubalis and Bos taurus, were used for in silico study. SWISS-PROT and BIOPEP protein libraries were accessed for prediction of peptide generation. Study observed gaps in the prediction versus actual results, which remain unaddressed in the literature. Many peptides obtained in vitro, were not reflected in in silico predictions. Differences in identified peptides in separate libraries were observed too. In in silico prediction, peptides with known biological activities were also not reflected. Predictions, towards generation of bioactive peptides, based upon in silico release of proteins and amino acid sequences from different sources and thereupon validation in relation to actual results has often been reported in research literature. Given that computer aided simulation for prediction purposes is an effective research direction, regular updating of protein libraries and an effectual integration, for more precise results, is critical. The gaps addressed between these two techniques of research, have not found any address in literature. Inclusion of more flexibility with the variables, within the tools being used for prediction, and a hierarchy based database with search options for various peptides, will further enhance the scope and strength of research. PMID:26344975

  19. In Silico and In Vitro Analysis of Bacoside A Aglycones and Its Derivatives as the Constituents Responsible for the Cognitive Effects of Bacopa monnieri

    PubMed Central

    Ramasamy, Seetha; Chin, Sek Peng; Sukumaran, Sri Devi; Buckle, Michael James Christopher; Kiew, Lik Voon; Chung, Lip Yong

    2015-01-01

    Bacopa monnieri has been used in Ayurvedic medicine to improve memory and cognition. The active constituent responsible for its pharmacological effects is bacoside A, a mixture of dammarane-type triterpenoid saponins containing sugar chains linked to a steroid aglycone skeleton. Triterpenoid saponins have been reported to be transformed in vivo to metabolites that give better biological activity and pharmacokinetic characteristics. Thus, the activities of the parent compounds (bacosides), aglycones (jujubogenin and pseudojujubogenin) and their derivatives (ebelin lactone and bacogenin A1) were compared using a combination of in silico and in vitro screening methods. The compounds were docked into 5-HT1A, 5-HT2A, D1, D2, M1 receptors and acetylcholinesterase (AChE) using AutoDock and their central nervous system (CNS) drug-like properties were determined using Discovery Studio molecular properties and ADMET descriptors. The compounds were screened in vitro using radioligand receptor binding and AChE inhibition assays. In silico studies showed that the parent bacosides were not able to dock into the chosen CNS targets and had poor molecular properties as a CNS drug. In contrast, the aglycones and their derivatives showed better binding affinity and good CNS drug-like properties, were well absorbed through the intestines and had good blood brain barrier (BBB) penetration. Among the compounds tested in vitro, ebelin lactone showed binding affinity towards M1 (Ki = 0.45 μM) and 5-HT2A (4.21 μM) receptors. Bacoside A and bacopaside X (9.06 μM) showed binding affinity towards the D1 receptor. None of the compounds showed any inhibitory activity against AChE. Since the stimulation of M1 and 5-HT2A receptors has been implicated in memory and cognition and ebelin lactone was shown to have the strongest binding energy, highest BBB penetration and binding affinity towards M1 and 5-HT2A receptors, we suggest that B. monnieri constituents may be transformed in vivo to the

  20. In Silico and In Vitro Analysis of Bacoside A Aglycones and Its Derivatives as the Constituents Responsible for the Cognitive Effects of Bacopa monnieri.

    PubMed

    Ramasamy, Seetha; Chin, Sek Peng; Sukumaran, Sri Devi; Buckle, Michael James Christopher; Kiew, Lik Voon; Chung, Lip Yong

    2015-01-01

    Bacopa monnieri has been used in Ayurvedic medicine to improve memory and cognition. The active constituent responsible for its pharmacological effects is bacoside A, a mixture of dammarane-type triterpenoid saponins containing sugar chains linked to a steroid aglycone skeleton. Triterpenoid saponins have been reported to be transformed in vivo to metabolites that give better biological activity and pharmacokinetic characteristics. Thus, the activities of the parent compounds (bacosides), aglycones (jujubogenin and pseudojujubogenin) and their derivatives (ebelin lactone and bacogenin A1) were compared using a combination of in silico and in vitro screening methods. The compounds were docked into 5-HT1A, 5-HT2A, D1, D2, M1 receptors and acetylcholinesterase (AChE) using AutoDock and their central nervous system (CNS) drug-like properties were determined using Discovery Studio molecular properties and ADMET descriptors. The compounds were screened in vitro using radioligand receptor binding and AChE inhibition assays. In silico studies showed that the parent bacosides were not able to dock into the chosen CNS targets and had poor molecular properties as a CNS drug. In contrast, the aglycones and their derivatives showed better binding affinity and good CNS drug-like properties, were well absorbed through the intestines and had good blood brain barrier (BBB) penetration. Among the compounds tested in vitro, ebelin lactone showed binding affinity towards M1 (Ki = 0.45 μM) and 5-HT2A (4.21 μM) receptors. Bacoside A and bacopaside X (9.06 μM) showed binding affinity towards the D1 receptor. None of the compounds showed any inhibitory activity against AChE. Since the stimulation of M1 and 5-HT2A receptors has been implicated in memory and cognition and ebelin lactone was shown to have the strongest binding energy, highest BBB penetration and binding affinity towards M1 and 5-HT2A receptors, we suggest that B. monnieri constituents may be transformed in vivo to the

  1. Pregnancy-Induced Gingivitis and OMICS in Dentistry: In Silico Modeling and in Vivo Prospective Validation of Estradiol-Modulated Inflammatory Biomarkers

    PubMed Central

    Zeidán-Chuliá, Fares; Könönen, Eija; Moreira, José C. F.; Liukkonen, Joonas; Sorsa, Timo; Gürsoy, Ulvi K.

    2014-01-01

    Abstract Pregnancy-associated gingivitis is a bacterial-induced inflammatory disease with a remarkably high prevalence ranging from 35% to 100% across studies. Yet little is known about the attendant mechanisms or diagnostic biomarkers that can help predict individual susceptibility for rational personalized medicine. We aimed to define inflammatory proteins in saliva, induced or inhibited by estradiol, as early diagnostic biomarkers or target proteins in relation to pregnancy-associated gingivitis. An in silico gene/protein interaction network model was developed by using the STITCH 3.1 with “experiments” and “databases” as input options and a confidence score of 0.700 (high confidence). Salivary estradiol, interleukin (IL)-1β and -8, myeloperoxidase (MPO), matrix metalloproteinase (MMP)-2, -8, and -9, and tissue inhibitor of matrix metalloproteinase (TIMP)-1 levels from 30 women were measured prospectively three times during pregnancy and twice during postpartum. In silico analysis revealed that estradiol interacts with IL-1β and -8 by an activation link when the “actions view” was consulted. In saliva, estradiol concentrations associated positively with TIMP-1 and negatively with MPO and MMP-8 concentrations. When the gingival bleeding on probing percentage (BOP%) was included in the model as an effect modifier, the only association, a negative one, was found between estradiol and MMP-8. Throughout gestation, estradiol modulates the inflammatory response by inhibiting neutrophilic enzymes, such as MMP-8. The interactions between salivary degradative enzymes and proinflammatory cytokines during pregnancy suggest promising ways to identify candidate biomarkers for pregnancy-associated gingivitis, and for personalized medicine in the field of dentistry. Finally, we call for greater investments in, and action for biomarker research in periodontology and dentistry that have surprisingly lagged behind in personalized medicine compared to other fields

  2. Lack of Detectable Allergenicity in Genetically Modified Maize Containing “Cry” Proteins as Compared to Native Maize Based on In Silico & In Vitro Analysis

    PubMed Central

    Mathur, Chandni; Kathuria, Pooran C.; Dahiya, Pushpa; Singh, Anand B.

    2015-01-01

    Background Genetically modified, (GM) crops with potential allergens must be evaluated for safety and endogenous IgE binding pattern compared to native variety, prior to market release. Objective To compare endogenous IgE binding proteins of three GM maize seeds containing Cry 1Ab,1Ac,1C transgenic proteins with non GM maize. Methods An integrated approach of in silico & in vitro methods was employed. Cry proteins were tested for presence of allergen sequence by FASTA in allergen databases. Biochemical assays for maize extracts were performed. Specific IgE (sIgE) and Immunoblot using food sensitized patients sera (n = 39) to non GM and GM maize antigens was performed. Results In silico approaches, confirmed for non sequence similarity of stated transgenic proteins in allergen databases. An insignificant (p> 0.05) variation in protein content between GM and non GM maize was observed. Simulated Gastric Fluid (SGF) revealed reduced number of stable protein fractions in GM then non GM maize which might be due to shift of constituent protein expression. Specific IgE values from patients showed insignificant difference in non GM and GM maize extracts. Five maize sensitized cases, recognized same 7 protein fractions of 88-28 kD as IgE bindng in both GM and non-GM maize, signifying absence of variation. Four of the reported IgE binding proteins were also found to be stable by SGF. Conclusion Cry proteins did not indicate any significant similarity of >35% in allergen databases. Immunoassays also did not identify appreciable differences in endogenous IgE binding in GM and non GM maize. PMID:25706412

  3. Antihyperglycemic and sub-chronic antidiabetic actions of morolic and moronic acids, in vitro and in silico inhibition of 11β-HSD 1.

    PubMed

    Ramírez-Espinosa, Juan José; García-Jiménez, Sara; Rios, Maria Yolanda; Medina-Franco, José L; López-Vallejo, Fabián; Webster, Scott P; Binnie, Margareth; Ibarra-Barajas, Maximiliano; Ortiz-Andrade, Rolffy; Estrada-Soto, Samuel

    2013-05-15

    Morolic (1) and moronic (2) acids are the main constituents of acetonic extract from Phoradendron reichenbachianum (Loranthaceae), a medicinal plant used in Mexico for the treatment of diabetes. The aim of the current study was to establish the sub-acute antidiabetic and antihyperlipidemic effects of compounds 1 and 2 over non insulin-dependent diabetic rat model. Also, to determine the antihyperglycemic action on normoglycemic rats by oral glucose tolerance test. Daily-administered morolic (1) and moronic (2) acids (50 mg/kg) significantly lowered the blood glucose levels at 60% since first day until tenth day after treatment than untreated group (p<0.05). Moreover, analyzed blood samples obtained from diabetic rats indicated that both compounds diminished plasmatic concentration of cholesterol (CHO) and triglycerides (TG), returning them to normal levels (p<0.05). Also, pretreatment with 50 mg/kg of each compound induced significant antihyperglycemic effect after glucose and sucrose loading (2 g/kg) compared with control group (p<0.05). In vitro studies showed that compounds 1 and 2 induced inhibition of 11β-HSD 1 activity at 10 μM. However, in silico analysis of the pentaclyclic triterpenic acids on 11β-HSD 1 revealed that all compounds had high docking scores and important interactions with the catalytic site allowing them to inhibit 11β-HSD 1 enzyme. In conclusion, morolic and moronic acids have shown sustained antidiabetic and antihyperglycemic action possibly mediated by an insulin sensitization with consequent changes of glucose, cholesterol and triglycerides, in part mediated by inhibition of 11β-HSD 1 as indicated by in vitro and in silico studies. PMID:23453304

  4. 28-Channel rotary transformer

    NASA Technical Reports Server (NTRS)

    Mclyman, W. T.

    1981-01-01

    Transformer transmits power and digital data across rotating interface. Array has many parallel data channels, each with potential l megabaud data rate. Ferrite-cored transformers are spaced along rotor; airgap between them reduces crosstalk.

  5. Equations For Rotary Transformers

    NASA Technical Reports Server (NTRS)

    Salomon, Phil M.; Wiktor, Peter J.; Marchetto, Carl A.

    1988-01-01

    Equations derived for input impedance, input power, and ratio of secondary current to primary current of rotary transformer. Used for quick analysis of transformer designs. Circuit model commonly used in textbooks on theory of ac circuits.

  6. Chemical Transformation Simulator

    EPA Science Inventory

    The Chemical Transformation Simulator (CTS) is a web-based, high-throughput screening tool that automates the calculation and collection of physicochemical properties for an organic chemical of interest and its predicted products resulting from transformations in environmental sy...

  7. Transformation of Pasteurella novicida

    PubMed Central

    Tyeryar, Franklin J.; Lawton, William D.

    1969-01-01

    Deoxyribonucleic acid from a streptomycin-resistant mutant of Pasteurella novicida transformed portions of P. novicida streptomycin-sensitive populations to streptomycin-resistant. Similarly, mutants auxotrophic for tryptophan or purine biosynthesis were also transformed to nutritional independence. PMID:5359612

  8. Tomographical transformation of Malvern spray measurements

    NASA Technical Reports Server (NTRS)

    Zhu, H. M.; Sun, T. Y.; Chigier, N.

    1987-01-01

    A new method is described which directly transforms Malvern line-integral data into point measurements of the radial drop mean size distribution and liquid volume concentration distribution. The transformed results have been compared with experimental point measurements by photography and the phase/Doppler spray analyzer. The comparison reveals the relation between point measurements and line-of-sight measurements. Three kinds of nozzles were investigated. After tomographical transformation of the Malvern results the different structures of the spray are revealed. A newly derived formula simplifies the transformation procedure. This method provides a direct means to extend the applicability of the Malvern particle sizer and has the potential to be developed for use in unsymmetric sprays.

  9. In-Silico Trials for Glucose Control in Hospitalized Patients with Type 2 Diabetes.

    PubMed

    Choi, Karam; Oh, Tae Jung; Lee, Jung Chan; Kim, Myungjoon; Kim, Hee Chan; Cho, Young Min; Kim, Sungwan

    2016-02-01

    Although various basal-bolus insulin therapy (BBIT) protocols have been used in the clinical environment, safer and more effective BBIT protocols are required for glucose control in hospitalized patients with type 2 diabetes (T2D). Modeling approaches could provide an evaluation environment for developing the optimal BBIT protocol prior to clinical trials at low cost and without risk of danger. In this study, an in-silico model was proposed to evaluate subcutaneous BBIT protocols in hospitalized patients with T2D. The proposed model was validated by comparing the BBIT protocol and sliding-scale insulin therapy (SSIT) protocol. The model was utilized for in-silico trials to compare the protocols of adjusting basal-insulin dose (BBIT1) versus adjusting total-daily-insulin dose (BBIT2). The model was also used to evaluate two different initial total-daily-insulin doses for various levels of renal function. The BBIT outcomes were superior to those of SSIT, which is consistent with earlier studies. BBIT2 also outperformed BBIT1, producing a decreased daily mean glucose level and longer time-in-target-range. Moreover, with a standard dose, the overall daily mean glucose levels reached the target range faster than with a reduced-dose for all degrees of renal function. The in-silico studies demonstrated several significant findings, including that the adjustment of total-daily-insulin dose is more effective than changes to basal-insulin dose alone. This research represents a first step toward the eventual development of an advanced model for evaluating various BBIT protocols. PMID:26839477

  10. An in silico model to demonstrate the effects of Maspin on cancer cell dynamics.

    PubMed

    Al-Mamun, M A; Farid, D M; Ravenhil, L; Hossain, M A; Fall, C; Bass, R

    2016-01-01

    Most cancer treatments efficacy depends on tumor metastasis suppression, where tumor suppressor genes play an important role. Maspin (Mammary Serine Protease Inhibitor), an non-inhibitory serpin has been reported as a potential tumor suppressor to influence cell migration, adhesion, proliferation and apoptosis in in vitro and in vivo experiments in last two decades. Lack of computational investigations hinders its ability to go through clinical trials. Previously, we reported first computational model for maspin effects on tumor growth using artificial neural network and cellular automata paradigm with in vitro data support. This paper extends the previous in silico model by encompassing how maspin influences cell migration and the cell-extracellular matrix interaction in subcellular level. A feedforward neural network was used to define each cell behavior (proliferation, quiescence, apoptosis) which followed a cell-cycle algorithm to show the microenvironment impacts over tumor growth. Furthermore, the model concentrates how the in silico experiments results can further confirm the fact that maspin reduces cell migration using specific in vitro data verification method. The data collected from in vitro and in silico experiments formulates an unsupervised learning problem which can be solved by using different clustering algorithms. A density based clustering technique was developed to measure the similarity between two datasets based on the number of links between instances. Our proposed clustering algorithm first finds the nearest neighbors of each instance, and then redefines the similarity between pairs of instances in terms of how many nearest neighbors share the two instances. The number of links between two instances is defined as the number of common neighbors they have. The results showed significant resemblances with in vitro experimental data. The results also offer a new insight into the dynamics of maspin and establish as a metastasis suppressor gene

  11. In Silico Design of Novel Anticoagulant Peptides targeting Blood Coagulation Factor VIIa

    PubMed Central

    Al-Amri, Manal S Q; Alrasadi, Khalid; Bayoumi, Riad; Banerjee, Yajnavalka

    2011-01-01

    Objectives: The coagulation cascade initiated during vascular injury prevents bleeding. Unwanted clot formation is however detrimental and requires the use of anticoagulants for prophylaxis and treatment. Anticoagulants targeting a specific step or an enzyme in the clotting process are most preferred as they minimise disadvantageous side-effects. A principal step in the discovery of novel anticoagulants encompasses the in silico design of potential leads. This study depicts the in silico design of peptide anticoagulants targeting coagulation factor VIIa. Methods: Applying the proline bracket rule and using various bioinformatics tools: the basic alignment search tool (BLAST) of National Center for Biotechnology Information; the T-coffee module provided by European Molecular Biology Laboratory-European Bioinformatics Institute, and several modules available on the ExPASy server, we designed five bivalent chimeric anticoagulants targeting factor VIIa, using factor VIIa inhibitors – hemextin A from Hemachatus haemachatus (African Ringhals cobra) venom and factor VIIa exosite-inhibitor peptide as templates. Six peptides were derived from hemextin A, which were concomitantly fused with factor VIIa exosite-inhibitor peptide intermediated by a polyalanine spacer, and analysed for structural stability using the SWISS-MODEL software developed at the Swiss Institute of Bioinformatics and WebLab ViewerPro (Version 4.2). Results: Twelve chimeric peptides were obtained; only five exhibited stable structures in silico. Conclusion: The five peptides obtained are probable anticoagulant leads that should be further evaluated using suitable in vitro and in vivo assays. Further, this study shows how simple web-based modules can be used for the rational design of probable leads targeting specific physiological molecular targets. PMID:21509213

  12. In-Silico Trials for Glucose Control in Hospitalized Patients with Type 2 Diabetes

    PubMed Central

    2016-01-01

    Although various basal-bolus insulin therapy (BBIT) protocols have been used in the clinical environment, safer and more effective BBIT protocols are required for glucose control in hospitalized patients with type 2 diabetes (T2D). Modeling approaches could provide an evaluation environment for developing the optimal BBIT protocol prior to clinical trials at low cost and without risk of danger. In this study, an in-silico model was proposed to evaluate subcutaneous BBIT protocols in hospitalized patients with T2D. The proposed model was validated by comparing the BBIT protocol and sliding-scale insulin therapy (SSIT) protocol. The model was utilized for in-silico trials to compare the protocols of adjusting basal-insulin dose (BBIT1) versus adjusting total-daily-insulin dose (BBIT2). The model was also used to evaluate two different initial total-daily-insulin doses for various levels of renal function. The BBIT outcomes were superior to those of SSIT, which is consistent with earlier studies. BBIT2 also outperformed BBIT1, producing a decreased daily mean glucose level and longer time-in-target-range. Moreover, with a standard dose, the overall daily mean glucose levels reached the target range faster than with a reduced-dose for all degrees of renal function. The in-silico studies demonstrated several significant findings, including that the adjustment of total-daily-insulin dose is more effective than changes to basal-insulin dose alone. This research represents a first step toward the eventual development of an advanced model for evaluating various BBIT protocols. PMID:26839477

  13. Accessing biological actions of Ganoderma secondary metabolites by in silico profiling

    PubMed Central

    Grienke, Ulrike; Kaserer, Teresa; Pfluger, Florian; Mair, Christina E.; Langer, Thierry; Schuster, Daniela; Rollinger, Judith M.

    2016-01-01

    The species complex around the medicinal fungus Ganoderma lucidum Karst. (Ganodermataceae) is widely known in traditional medicines as well as in modern applications such as functional food or nutraceuticals. A considerable number of publications reflects its abundance and variety in biological actions either provoked by primary metabolites such as polysaccharides or secondary metabolites such as lanostane-type triterpenes. However, due to this remarkable amount of information, a rationalization of the individual Ganoderma constituents to biological actions on a molecular level is quite challenging. To overcome this issue, a database was generated containing meta-information, i.e. chemical structures and biological actions of hitherto identified Ganoderma constituents (279). This was followed by a computational approach subjecting this 3D multi-conformational molecular dataset to in silico parallel screening against an in-house collection of validated structure- and ligand-based 3D pharmacophore models. The predictive power of the evaluated in silico tools and hints from traditional application fields served as criteria for the model selection. Thus, we focused on representative druggable targets in the field of viral infections (5) and diseases related to the metabolic syndrome (22). The results obtained from this in silico approach were compared to bioactivity data available from the literature to distinguish between true and false positives or negatives. 89 and 197 Ganoderma compounds were predicted as ligands of at least one of the selected pharmacological targets in the antiviral and the metabolic syndrome screening, respectively. Among them only a minority of individual compounds (around 10%) has ever been investigated on these targets or for the associated biological activity. Accordingly, this study discloses putative ligand target interactions for a plethora of Ganoderma constituents in the empirically manifested field of viral diseases and metabolic

  14. In Silico Modeling of Novel Drug Ligands for Treatment of Concussion Associated Tauopathy.

    PubMed

    Zhao, Wei; Ho, Lap; Wang, Jun; Bi, Weina; Yemul, Shrishailam; Ward, Libby; Freire, Daniel; Mazzola, Paolo; Brathwaite, Justin; Mezei, Mihaly; Sanchez, Roberto; Elder, Gregory A; Pasinetti, Giulio Maria

    2016-10-01

    The objective of this study was to develop an in silico screening model for characterization of potential novel ligands from commercial drug libraries able to functionally activate certain olfactory receptors (ORs), which are members of the class A rhodopsin-like family of G protein couple receptors (GPCRs), in the brain of murine models of concussion. We previously found that concussions may significantly influence expression of certain ORs, for example, OR4M1 in subjects with a history of concussion/traumatic brain injury (TBI). In this study, we built a 3-D OR4M1 model and used it in in silico screening of potential novel ligands from commercial drug libraries. We report that in vitro activation of OR4M1 with the commercially available ZINC library compound 10915775 led to a significant attenuation of abnormal tau phosphorylation in embryonic cortico-hippocampal neuronal cultures derived from NSE-OR4M1 transgenic mice, possibly through modulation of the JNK signaling pathway. The attenuation of abnormal tau phosphorylation was rather selective since ZINC10915775 significantly decreased tau phosphorylation on tau Ser202/T205 (AT8 epitope) and tau Thr212/Ser214 (AT100 epitope), but not on tau Ser396/404 (PHF-1 epitope). Moreover, no response of ZINC10915775 was found in control hippocampal neuronal cultures derived from wild type littermates. Our in silico model provides novel means to pharmacologically modulate select ubiquitously expressed ORs in the brain through high affinity ligand activation to prevent and eventually to treat concussion induced down regulation of ORs and subsequent cascade of tau pathology. J. Cell. Biochem. 117: 2241-2248, 2016. © 2016 Wiley Periodicals, Inc. PMID:26910498

  15. Pediatric in vitro and in silico models of deposition via oral and nasal inhalation.

    PubMed

    Carrigy, Nicholas B; Ruzycki, Conor A; Golshahi, Laleh; Finlay, Warren H

    2014-06-01

    Respiratory tract deposition models provide a useful method for optimizing the design and administration of inhaled pharmaceutical aerosols, and can be useful for estimating exposure risks to inhaled particulate matter. As aerosol must first pass through the extrathoracic region prior to reaching the lungs, deposition in this region plays an important role in both cases. Compared to adults, much less extrathoracic deposition data are available with pediatric subjects. Recently, progress in magnetic resonance imaging and computed tomography scans to develop pediatric extrathoracic airway replicas has facilitated addressing this issue. Indeed, the use of realistic replicas for benchtop inhaler testing is now relatively common during the development and in vitro evaluation of pediatric respiratory drug delivery devices. Recently, in vitro empirical modeling studies using a moderate number of these realistic replicas have related airway geometry, particle size, fluid properties, and flow rate to extrathoracic deposition. Idealized geometries provide a standardized platform for inhaler testing and exposure risk assessment and have been designed to mimic average in vitro deposition in infants and children by replicating representative average geometrical dimensions. In silico mathematical models have used morphometric data and aerosol physics to illustrate the relative importance of different deposition mechanisms on respiratory tract deposition. Computational fluid dynamics simulations allow for the quantification of local deposition patterns and an in-depth examination of aerosol behavior in the respiratory tract. Recent studies have used both in vitro and in silico deposition measurements in realistic pediatric airway geometries to some success. This article reviews the current understanding of pediatric in vitro and in silico deposition modeling via oral and nasal inhalation. PMID:24870701

  16. Shiftable multiscale transforms

    NASA Technical Reports Server (NTRS)

    Simoncelli, Eero P.; Freeman, William T.; Adelson, Edward H.; Heeger, David J.

    1992-01-01

    A type of translational invariance, referred to as shiftability, is defined for wavelet transforms. The property of shiftability is first discussed with respect to individual parameters: spatial position, orientation, and scale. The discussion then focuses on transformations that are simultaneously shiftable with respect to subsets of these parameters. It is shown that the critical sampling condition on the wavelet transforms must be relaxed to achieve shiftability. Two example transforms are implemented and applied to several signal and image processing problems.

  17. Active Components of Essential Oils as Anti-Obesity Potential Drugs Investigated by in Silico Techniques.

    PubMed

    Costa, Giosuè; Gidaro, Maria Concetta; Vullo, Daniela; Supuran, Claudiu T; Alcaro, Stefano

    2016-07-01

    In this study, for the first time, we have considered essential oils (EOs) as possible resources of carbonic anhydrase inhibitors (CAIs), in particular against the mitochondrial isoform VA that, actually, represents an innovative target for the obesity treatment. In silico structure-based virtual screening was performed in order to speed up the identification of promising antiobesity agents. The potential hit compounds were submitted to in vitro assays and experimental results, corroborated by molecular modeling studies, showed EOs components as a new class of CAIs with a competitive mechanism of action due to the zinc ion coordination within the active sites of these metallo-enzymes. PMID:27268752

  18. In Silico Modelling of Treatment-Induced Tumour Cell Kill: Developments and Advances

    PubMed Central

    Marcu, Loredana G.; Harriss-Phillips, Wendy M.

    2012-01-01

    Mathematical and stochastic computer (in silico) models of tumour growth and treatment response of the past and current eras are presented, outlining the aims of the models, model methodology, the key parameters used to describe the tumour system, and treatment modality applied, as well as reported outcomes from simulations. Fractionated radiotherapy, chemotherapy, and combined therapies are reviewed, providing a comprehensive overview of the modelling literature for current modellers and radiobiologists to ignite the interest of other computational scientists and health professionals of the ever evolving and clinically relevant field of tumour modelling. PMID:22852024

  19. In silico experiments of single-chain antibody fragment against drugs of abuse

    PubMed Central

    Hu, Guodong; Chen, L. Y.

    2010-01-01

    SUMMARY Three sets of in silico experiments have been conducted to elucidate the binding mechanics of two drugs, (+)-methamphetamine (METH) and amphetamine (AMP) to the single-chain variable fragment (scFv) recently engineered from anti-METH monoclonal antibody mAb6H4 (IgG, κ light chain, Kd = 11nM). The first set of in silico experiments are long time equilibration runs of scFv:drug complexes and of drug-free scFv both in solution. They demonstrate how the solution structures of scFv deviate from its crystallographic form with or without drug molecules bound to it. And they lead to the prediction that the Arrhenius activation barrier is nearly zero for transitions from the dissociated state to the bound state. The second set of in silico experiments are nonequilibrium dynamics of pulling the drug molecules out of the binding pocket of scFv and the equilibration runs for drugs to fall back into binding pocket. They demonstrate that extra water molecules (in addition to the two crystallographic waters) exist inside the binding pocket, underneath the drug molecules. These extra waters must have been evaporated from the binding pockets during the crystallization process of the in vitro experiments of structural determination. The third set of in silico experiments are nonequilibrium steered molecular dynamics simulations to determine the absolute binding free energies of METH and AMP to scFv. The center-of-mass of a drug molecule (METH or AMP) is steered (pulled) towards (forward) and away from (reverse) the binding site, sampling forward and reverse pulling paths. Mechanic work is measured along the pulling paths. The work measurements are averaged through the Brownian dynamics fluctuation dissipation theorem to produce the free-energy profiles of the scFv:drug complexes as a function of the drug-scFv separation. These experiments lead to the theoretical prediction of absolute binding energies of METH and AMP that are in agreement with the in vitro experimental

  20. Integrating in Silico and in Vitro Approaches To Predict Drug Accessibility to the Central Nervous System.

    PubMed

    Zhang, Yan-Yan; Liu, Houfu; Summerfield, Scott G; Luscombe, Christopher N; Sahi, Jasminder

    2016-05-01

    Estimation of uptake across the blood-brain barrier (BBB) is key to designing central nervous system (CNS) therapeutics. In silico approaches ranging from physicochemical rules to quantitative structure-activity relationship (QSAR) models are utilized to predict potential for CNS penetration of new chemical entities. However, there are still gaps in our knowledge of (1) the relationship between marketed human drug derived CNS-accessible chemical space and preclinical neuropharmacokinetic (neuroPK) data, (2) interpretability of the selected physicochemical descriptors, and (3) correlation of the in vitro human P-glycoprotein (P-gp) efflux ratio (ER) and in vivo rodent unbound brain-to-blood ratio (Kp,uu), as these are assays routinely used to predict clinical CNS exposure, during drug discovery. To close these gaps, we explored the CNS druglike property boundaries of 920 market oral drugs (315 CNS and 605 non-CNS) and 846 compounds (54 CNS drugs and 792 proprietary GlaxoSmithKline compounds) with available rat Kp,uu data. The exact permeability coefficient (Pexact) and P-gp ER were determined for 176 compounds from the rat Kp,uu data set. Receiver operating characteristic curves were performed to evaluate the predictive power of human P-gp ER for rat Kp,uu. Our data demonstrates that simple physicochemical rules (most acidic pKa ≥ 9.5 and TPSA < 100) in combination with P-gp ER < 1.5 provide mechanistic insights for filtering BBB permeable compounds. For comparison, six classification modeling methods were investigated using multiple sets of in silico molecular descriptors. We present a random forest model with excellent predictive power (∼0.75 overall accuracy) using the rat neuroPK data set. We also observed good concordance between the structural interpretation results and physicochemical descriptor importance from the Kp,uu classification QSAR model. In summary, we propose a novel, hybrid in silico/in vitro approach and an in silico screening model for the

  1. Microbial Consortia Engineering for Cellular Factories: in vitro to in silico systems

    PubMed Central

    Bernstein, Hans C; Carlson, Ross P

    2012-01-01

    This mini-review discusses the current state of experimental and computational microbial consortia engineering with a focus on cellular factories. A discussion of promising ecological theories central to community resource usage is presented to facilitate interpretation of consortial designs. Recent case studies exemplifying different resource usage motifs and consortial assembly templates are presented. The review also highlights in silico approaches to design and to analyze consortia with an emphasis on stoichiometric modeling methods. The discipline of microbial consortia engineering possesses a widely accepted potential to generate highly novel and effective bio-catalysts for applications from biofuels to specialty chemicals to enhanced mineral recovery. PMID:24688677

  2. The Use of In Silico Models Within a Large Pharmaceutical Company.

    PubMed

    Brigo, Alessandro; Muster, Wolfgang

    2016-01-01

    The present contribution describes how in silico models are applied at different stages of the drug discovery process in the pharmaceutical industry. A thorough description of the most relevant computational methods and tools is given along with an in-depth evaluation of their performance in the context of potential genotoxic impurities assessment.The challenges of predicting the outcome of highly complex studies are discussed followed by considerations on how novel ways to manage, store, share and analyze data may advance knowledge and facilitate modeling efforts. PMID:27311478

  3. In Silico Approaches and the Role of Ontologies in Aging Research

    PubMed Central

    Boerries, Melanie; Busch, Hauke; de Grey, Aubrey; Hahn, Udo; Hiller, Thomas; Hoeflich, Andreas; Jansen, Ludger; Janssens, Georges E.; Kaleta, Christoph; Meinema, Anne C.; Schäuble, Sascha; Simm, Andreas; Schofield, Paul N.; Smith, Barry; Sühnel, Juergen; Vera, Julio; Wagner, Wolfgang; Wönne, Eva C.; Wuttke, Daniel

    2013-01-01

    Abstract The 2013 Rostock Symposium on Systems Biology and Bioinformatics in Aging Research was again dedicated to dissecting the aging process using in silico means. A particular focus was on ontologies, because these are a key technology to systematically integrate heterogeneous information about the aging process. Related topics were databases and data integration. Other talks tackled modeling issues and applications, the latter including talks focused on marker development and cellular stress as well as on diseases, in particular on diseases of kidney and skin. PMID:24188080

  4. In silico approaches and the role of ontologies in aging research.

    PubMed

    Fuellen, Georg; Boerries, Melanie; Busch, Hauke; de Grey, Aubrey; Hahn, Udo; Hiller, Thomas; Hoeflich, Andreas; Jansen, Ludger; Janssens, Georges E; Kaleta, Christoph; Meinema, Anne C; Schäuble, Sascha; Simm, Andreas; Schofield, Paul N; Smith, Barry; Sühnel, Juergen; Vera, Julio; Wagner, Wolfgang; Wönne, Eva C; Wuttke, Daniel

    2013-12-01

    The 2013 Rostock Symposium on Systems Biology and Bioinformatics in Aging Research was again dedicated to dissecting the aging process using in silico means. A particular focus was on ontologies, because these are a key technology to systematically integrate heterogeneous information about the aging process. Related topics were databases and data integration. Other talks tackled modeling issues and applications, the latter including talks focused on marker development and cellular stress as well as on diseases, in particular on diseases of kidney and skin. PMID:24188080

  5. Achieving Perspective Transformation.

    ERIC Educational Resources Information Center

    Nowak, Jens

    Perspective transformation is a consciously achieved state in which the individual's perspective on life is transformed. The new perspective serves as a vantage point for life's actions and interactions, affecting the way life is lived. Three conditions are basic to achieving perspective transformation: (1) "feeling" experience, i.e., getting in…

  6. Localization and in silico study of the vegetative insecticidal proteins Vip2S-Vip1S of Bacillus thuringiensis.

    PubMed

    Sellami, Sameh; Jemli, Sonia; Abdelmalek, Nouha; Dabbéche, Emna; Jamoussi, Kaïs

    2016-10-01

    The Bacillus thuringiensis S1/4 strain was previously found to harbour vip1S, vip2S, and vip3 genes. Its plasmid curing led to the obtaining of four partially cured strains S1/4-2, S1/4-3, S1/4-7, and S1/4-9 (vip2S-vip1S (-), vip3 (+)), one strain S1/4-4 (vip2S-vip1S (+), vip3 (-)), and S1/4-0 strain lacking the three genes. Using these derivative strains as templates, PCR amplification and southern blot assay revealed that vip2S-vip1S operon and vip3 gene were localized on two different large plasmids. Bioinformatics studies showed that vip2S (1.356 kb), and vip1S (2.637 kb) genes are encoding by an operon consisting of two ORFs separated by an intergenic spacer of 4bp. Using the InterPro tool, Vip2S was found to belong to the family of Binary exotoxin A and Vip1S to bacterial exotoxin B. In silico modeling indicated that the 3D structure of Vip2S is a mixed α/β protein and proposed 3D-model of Vip1S. Bioassays of the partially cured strains supernatants showed a weak toxicity of S1/4-4 to the lepidopteran Spodoptera littoralis comparing to a better effect of S1/4-2, S1/4-3, S1/4-7, and S1/4-9, suggesting its eventual contribution to the toxicity. Nevertheless, the concentrated supernatant of S1/4-4 strain was not toxic against the coleopteran Tribolium castaneum. PMID:27264647

  7. In Silico Analysis of Usher Encoding Genes in Klebsiella pneumoniae and Characterization of Their Role in Adhesion and Colonization

    PubMed Central

    Khater, Fida; Balestrino, Damien; Charbonnel, Nicolas; Dufayard, Jean François; Brisse, Sylvain; Forestier, Christiane

    2015-01-01

    Chaperone/usher (CU) assembly pathway is used by a wide range of Enterobacteriaceae to assemble adhesive surface structures called pili or fimbriae that play a role in bacteria-host cell interactions. In silico analysis revealed that the genome of Klebsiella pneumoniae LM21 harbors eight chromosomal CU loci belonging to γκп and ϭ clusters. Of these, only two correspond to previously described operons, namely type 1 and type 3-encoding operons. Isogenic usher deletion mutants of K. pneumoniae LM21 were constructed for each locus and their role in adhesion to animal (Intestine 407) and plant (Arabidopsis thaliana) cells, biofilm formation and murine intestinal colonization was investigated. Type 3 pili usher deleted mutant was impaired in all assays, whereas type 1 pili usher deleted mutant only showed attenuation in adhesion to plant cells and in intestinal colonization. The LM21ΔkpjC mutant was impaired in its capacity to adhere to Arabidopsis cells and to colonize the murine intestine, either alone or in co-inoculation experiments. Deletion of LM21kpgC induced a significant decrease in biofilm formation, in adhesion to animal cells and in colonization of the mice intestine. The LM21∆kpaC and LM21∆kpeC mutants were only attenuated in biofilm formation and the adhesion abilities to Arabidopsis cells, respectively. No clear in vitro or in vivo effect was observed for LM21∆kpbC and LM21∆kpdC mutants. The multiplicity of CU loci in K. pneumoniae genome and their specific adhesion pattern probably reflect the ability of the bacteria to adhere to different substrates in its diverse ecological niches. PMID:25751658

  8. Exonic Splicing Mutations Are More Prevalent than Currently Estimated and Can Be Predicted by Using In Silico Tools

    PubMed Central

    Soukarieh, Omar; Gaildrat, Pascaline; Hamieh, Mohamad; Drouet, Aurélie; Baert-Desurmont, Stéphanie; Frébourg, Thierry; Tosi, Mario; Martins, Alexandra

    2016-01-01

    The identification of a causal mutation is essential for molecular diagnosis and clinical management of many genetic disorders. However, even if next-generation exome sequencing has greatly improved the detection of nucleotide changes, the biological interpretation of most exonic variants remains challenging. Moreover, particular attention is typically given to protein-coding changes often neglecting the potential impact of exonic variants on RNA splicing. Here, we used the exon 10 of MLH1, a gene implicated in hereditary cancer, as a model system to assess the prevalence of RNA splicing mutations among all single-nucleotide variants identified in a given exon. We performed comprehensive minigene assays and analyzed patient’s RNA when available. Our study revealed a staggering number of splicing mutations in MLH1 exon 10 (77% of the 22 analyzed variants), including mutations directly affecting splice sites and, particularly, mutations altering potential splicing regulatory elements (ESRs). We then used this thoroughly characterized dataset, together with experimental data derived from previous studies on BRCA1, BRCA2, CFTR and NF1, to evaluate the predictive power of 3 in silico approaches recently described as promising tools for pinpointing ESR-mutations. Our results indicate that ΔtESRseq and ΔHZEI-based approaches not only discriminate which variants affect splicing, but also predict the direction and severity of the induced splicing defects. In contrast, the ΔΨ-based approach did not show a compelling predictive power. Our data indicates that exonic splicing mutations are more prevalent than currently appreciated and that they can now be predicted by using bioinformatics methods. These findings have implications for all genetically-caused diseases. PMID:26761715

  9. Genome-scale metabolic network reconstruction and in silico flux analysis of the thermophilic bacterium Thermus thermophilus HB27

    PubMed Central

    2014-01-01

    Background Thermus thermophilus, an extremely thermophilic bacterium, has been widely recognized as a model organism for studying how microbes can survive and adapt under high temperature environment. However, the thermotolerant mechanisms and cellular metabolism still remains mostly unravelled. Thus, it is highly required to consider systems biological approaches where T. thermophilus metabolic network model can be employed together with high throughput experimental data for elucidating its physiological characteristics under such harsh conditions. Results We reconstructed a genome-scale metabolic model of T. thermophilus, iTT548, the first ever large-scale network of a thermophilic bacterium, accounting for 548 unique genes, 796 reactions and 635 unique metabolites. Our initial comparative analysis of the model with Escherichia coli has revealed several distinctive metabolic reactions, mainly in amino acid metabolism and carotenoid biosynthesis, producing relevant compounds to retain the cellular membrane for withstanding high temperature. Constraints-based flux analysis was, then, applied to simulate the metabolic state in glucose minimal and amino acid rich media. Remarkably, resulting growth predictions were highly consistent with the experimental observations. The subsequent comparative flux analysis under different environmental conditions highlighted that the cells consumed branched chain amino acids preferably and utilized them directly in the relevant anabolic pathways for the fatty acid synthesis. Finally, gene essentiality study was also conducted via single gene deletion analysis, to identify the conditional essential genes in glucose minimal and complex media. Conclusions The reconstructed genome-scale metabolic model elucidates the phenotypes of T. thermophilus, thus allowing us to gain valuable insights into its cellular metabolism through in silico simulations. The information obtained from such analysis would not only shed light on the

  10. In silico analysis and recombinant expression of BamA protein as a universal vaccine against Escherichia coli in mice.

    PubMed

    Guan, Qingfeng; Wang, Xiao; Wang, Xiumin; Teng, Da; Wang, Jianhua

    2016-06-01

    Colibacillosis, caused by pathogenic Escherichia coli, is a common disease in animals and human worldwide with extensive losses in breeding industry and with millions of people death annually. There is thus an urgent need for the development of universal vaccines against colibacillosis. In this study, the BamA protein was analyzed in silico for sequence homology, physicochemical properties, allergenic prediction, and epitopes prediction. The BamA protein (containing 286 amino acids) clusters in E. coli were retrieved in UniProtKB database, in which 81.7 % sequences were identical (Uniref entry A7ZHR7), and sequences with 94.82 % identity were above 93.4 %. Moreover, BamA was highly conserved among Salmonella and Shigella and has no allergenicity to mice and human. The epitopes of BamA were located principally in periplasm and extracellular domain. Surf_Ag_VNR domain (at position 448-810 aa) of BamA was expressed, purified, and then used for immunization of mice. Titers of the rBamA sera were 1:736,000 and 1:152,000 against rBamA and E. coli and over 1:27,000 against Salmonella and Shigella. Opsonophagocytosis result revealed that the rBamA sera strengthened the phagocytic activity of neutrophils against E. coli. The survival rate of mice vaccinated with rBamA and PBS was 80 and 20 %, respectively. These data indicated that BamA could serve as a promising universal vaccine candidate for the development of a protective subunit vaccine against bacterial infection. Thus, the above protocol would provide more feasible technical clues and choices for available control of pathogenic E. coli, Salmonella, and Shigella. PMID:27020285

  11. Structural and functional characterization of pathogenic non- synonymous genetic mutations of human insulin-degrading enzyme by in silico methods.

    PubMed

    Shaik, Noor A; Kaleemuddin, Mohammed; Banaganapalli, Babajan; Khan, Fazal; Shaik, Nazia S; Ajabnoor, Ghada; Al-Harthi, Sameer E; Bondagji, Nabeel; Al-Aama, Jumana Y; Elango, Ramu

    2014-04-01

    Insulin-degrading enzyme (IDE) is a key protease involved in degrading insulin and amyloid peptides in human body. Several non-synonymous genetic mutations of IDE gene have been recently associated with susceptibility to both diabetes and Alzheimer's diseases. However, the consequence of these mutations on the structure of IDE protein and its substrate binding characteristics is not well elucidated. The computational investigation of genetic mutation consequences on structural level of protein is recently found to be an effective alternate to traditional in vivo and in vitro approaches. Hence, by using a combination of empirical rule and support vector machine based in silico algorithms, this study was able to identify that the pathogenic nonsynonymous genetic mutations corresponding to p.I54F, p.P122T, p.T533R, p.P581A and p.Y609A have more potential role in structural and functional deviations of IDE activity. Moreover, molecular modeling and secondary structure analysis have also confirmed their impact on the stability and secondary properties of IDE protein. The molecular docking analysis of IDE with combinational substrates has revealed that peptide inhibitors compared to small non-peptide inhibitor molecules possess good inhibitory activity towards mutant IDE. This finding may pave a way to design novel potential small peptide inhibitors for mutant IDE. Additionally by un-translated region (UTR) scanning analysis, two regulatory pathogenic genetic mutations i.e., rs5786997 (3' UTR) and rs4646954 (5' UTR), which can influence the translation pattern of IDE gene through sequence alteration of upstream-Open Reading Frame and Internal Ribosome Entry Site elements were identified. Our findings are expected to help in narrowing down the number of IDE genetic variants to be screened for disease association studies and also to select better competitive inhibitors for IDE related diseases. PMID:24059301

  12. Transformation of oil palm using Agrobacterium tumefaciens.

    PubMed

    Izawati, Abang Masli Dayang; Parveez, Ghulam Kadir Ahmad; Masani, Mat Yunus Abdul

    2012-01-01

    Transgenic oil palm (Elaeis guineensis Jacq.) plantlets are regenerated after Agrobacterium tumefaciens-mediated transformation of embryogenic calli derived from young leaves of oil palm. The calli are transformed with an Agrobacterium strain, LBA4404, harboring the plasmid pUBA, which carries a selectable marker gene (bar) for resistance to the herbicide Basta and is driven by a maize ubiquitin promoter. Modifications of the transformation method, treatment of the target tissues using acetosyringone, exposure to a plasmolysis medium, and physical injury via biolistics are applied. The main reasons for such modifications are to activate the bacterial virulence system and, subsequently, to increase the transformation efficiency. Transgenic oil palm cells are selected and regenerated on a medium containing herbicide Basta. Molecular analyses revealed the presence and integration of the introduced bar gene into the genome of the transformants. PMID:22351008

  13. Entangled Husimi Distribution and Complex Wavelet Transformation

    NASA Astrophysics Data System (ADS)

    Hu, Li-Yun; Fan, Hong-Yi

    2010-05-01

    Similar in spirit to the preceding work (Int. J. Theor. Phys. 48:1539, 2009) where the relationship between wavelet transformation and Husimi distribution function is revealed, we study this kind of relationship to the entangled case. We find that the optical complex wavelet transformation can be used to study the entangled Husimi distribution function in phase space theory of quantum optics. We prove that, up to a Gaussian function, the entangled Husimi distribution function of a two-mode quantum state | ψ> is just the modulus square of the complex wavelet transform of e^{-\\vert η \\vert 2/2} with ψ( η) being the mother wavelet.

  14. Note: Tesla transformer damping

    NASA Astrophysics Data System (ADS)

    Reed, J. L.

    2012-07-01

    Unexpected heavy damping in the two winding Tesla pulse transformer is shown to be due to small primary inductances. A small primary inductance is a necessary condition of operability, but is also a refractory inefficiency. A 30% performance loss is demonstrated using a typical "spiral strip" transformer. The loss is investigated by examining damping terms added to the transformer's governing equations. A significant alteration of the transformer's architecture is suggested to mitigate these losses. Experimental and simulated data comparing the 2 and 3 winding transformers are cited to support the suggestion.

  15. Transformation pathways of liposomes.

    PubMed

    Hotani, H

    1984-09-01

    Liposomes undergoing transformation were observed by dark-field light microscopy in order to study the role of lipid in morphogenesis of biological vesicular structures. Liposomes were found to transform sequentially in a well-defined manner through one of several transformation pathways. A circular biconcave form was an initial shape in all the pathways and it transformed into a stable thin flexible filament or small spheres via a variety of regularly shaped vesicles which possessed geometrical symmetry. The transformation was reversible up to a certain point in each pathway. Osmotic pressure was found to be the driving force for the transformations. Biological membrane vesicles such as trypsinized red cell ghosts also transformed by similar pathways. PMID:6548263

  16. Interaction of Catechu Dye with DNA: Spectroscopic and In Silico Approach.

    PubMed

    Hemachandran, Hridya; Anantharaman, Amrita; Priya, Rajendra Rao; Doss, George Priya; Siva, Ramamoorthy

    2016-01-01

    Catechin, a yellow colored molecule obtained from the wood of Acacia catechu was analyzed for its interaction with synthetic DNA duplexes using spectroscopic analysis. UV-Visible spectroscopic analysis revealed the non-intercalative binding mode. Fourier Transform Infrared spectroscopy (FTIR) analysis expose chemical shift indicated by various vibrational stretches and an increase in the intensity of base stacking was observed by Circular Dichroism (CD), respectively. This inference was further confirmed through nuclear staining technique and also in electrophoretic technique; the dye quenches the fluorescent intensity of ethidium bromide. The result of fluorescence spectroscopy was in concordance with the electrophoretic technique. In addition, the spectroscopic results were in accordance with the molecular docking studies of specific catechin compound from the catechu dye with CT-DNA. This kind of site specificity is a gain in the medicinal field as the drug can be DNA targeted for cancer therapeutics. The present work reveals that catechu dye has a noteworthy application in the field of medical bioscience. PMID:26913965

  17. Cells transformed by murine herpesvirus 68 (MHV-68) release compounds with transforming and transformed phenotype suppressing activity resembling growth factors.

    PubMed

    Šupolíková, M; Staňová, A Vojs; Kúdelová, M; Marák, J; Zelník, V; Golais, F

    2015-12-01

    In this study, we investigated the medium of three cell lines transformed with murine herpesvirus 68 (MHV-68) in vitro and in vivo, 68/HDF, 68/NIH3T3, and S11E, for the presence of compounds resembling growth factors of some herpesviruses which have displayed transforming and transformed phenotype suppressing activity in normal and tumor cells. When any of spent medium was added to cell culture we observed the onset of transformed phenotype in baby hamster kidney cells (BHK-21) cells and transformed phenotype suppressing activity in tumor human epithelial cells (HeLa). In media tested, we have identified the presence of putative growth factor related to MHV-68 (MHGF-68). Its bivalent properties have been blocked entirely by antisera against MHV-68 and two monoclonal antibodies against glycoprotein B (gB) of MHV-68 suggesting viral origin of MHGF-68. The results of initial efforts to separate MHGF-68 on FPLC Sephadex G15 column in the absence of salts revealed the loss of its transforming activity but transformed phenotype suppressing activity retained. On the other hand, the use of methanol-water mobile phase on RP-HPLC C18 column allowed separation of MHGF-68 to two compounds. Both separated fractions, had only the transforming activity to normal cells. Further experiments exploring the nature and the structure of hitherto unknown MHGF-68 are now in the progress to characterize its molecular and biological properties. PMID:26666191

  18. In silico Identification and Characterization of Protein-Ligand Binding Sites.

    PubMed

    Roche, Daniel Barry; McGuffin, Liam James

    2016-01-01

    Protein-ligand binding site prediction methods aim to predict, from amino acid sequence, protein-ligand interactions, putative ligands, and ligand binding site residues using either sequence information, structural information, or a combination of both. In silico characterization of protein-ligand interactions has become extremely important to help determine a protein's functionality, as in vivo-based functional elucidation is unable to keep pace with the current growth of sequence databases. Additionally, in vitro biochemical functional elucidation is time-consuming, costly, and may not be feasible for large-scale analysis, such as drug discovery. Thus, in silico prediction of protein-ligand interactions must be utilized to aid in functional elucidation. Here, we briefly discuss protein function prediction, prediction of protein-ligand interactions, the Critical Assessment of Techniques for Protein Structure Prediction (CASP) and the Continuous Automated EvaluatiOn (CAMEO) competitions, along with their role in shaping the field. We also discuss, in detail, our cutting-edge web-server method, FunFOLD for the structurally informed prediction of protein-ligand interactions. Furthermore, we provide a step-by-step guide on using the FunFOLD web server and FunFOLD3 downloadable application, along with some real world examples, where the FunFOLD methods have been used to aid functional elucidation. PMID:27094282

  19. Animal and in silico models for the study of sarcomeric cardiomyopathies

    PubMed Central

    Duncker, Dirk J.; Bakkers, Jeroen; Brundel, Bianca J.; Robbins, Jeff; Tardiff, Jil C.; Carrier, Lucie

    2015-01-01

    Over the past decade, our understanding of cardiomyopathies has improved dramatically, due to improvements in screening and detection of gene defects in the human genome as well as a variety of novel animal models (mouse, zebrafish, and drosophila) and in silico computational models. These novel experimental tools have created a platform that is highly complementary to the naturally occurring cardiomyopathies in cats and dogs that had been available for some time. A fully integrative approach, which incorporates all these modalities, is likely required for significant steps forward in understanding the molecular underpinnings and pathogenesis of cardiomyopathies. Finally, novel technologies, including CRISPR/Cas9, which have already been proved to work in zebrafish, are currently being employed to engineer sarcomeric cardiomyopathy in larger animals, including pigs and non-human primates. In the mouse, the increased speed with which these techniques can be employed to engineer precise ‘knock-in’ models that previously took years to make via multiple rounds of homologous recombination-based gene targeting promises multiple and precise models of human cardiac disease for future study. Such novel genetically engineered animal models recapitulating human sarcomeric protein defects will help bridging the gap to translate therapeutic targets from small animal and in silico models to the human patient with sarcomeric cardiomyopathy. PMID:25600962

  20. Toward Building Hybrid Biological/in silico Neural Networks for Motor Neuroprosthetic Control

    PubMed Central

    Kocaturk, Mehmet; Gulcur, Halil Ozcan; Canbeyli, Resit

    2015-01-01

    In this article, we introduce the Bioinspired Neuroprosthetic Design Environment (BNDE) as a practical platform for the development of novel brain–machine interface (BMI) controllers, which are based on spiking model neurons. We built the BNDE around a hard real-time system so that it is capable of creating simulated synapses from extracellularly recorded neurons to model neurons. In order to evaluate the practicality of the BNDE for neuroprosthetic control experiments, a novel, adaptive BMI controller was developed and tested using real-time closed-loop simulations. The present controller consists of two in silico medium spiny neurons, which receive simulated synaptic inputs from recorded motor cortical neurons. In the closed-loop simulations, the recordings from the cortical neurons were imitated using an external, hardware-based neural signal synthesizer. By implementing a reward-modulated spike timing-dependent plasticity rule, the controller achieved perfect target reach accuracy for a two-target reaching task in one-dimensional space. The BNDE combines the flexibility of software-based spiking neural network (SNN) simulations with powerful online data visualization tools and is a low-cost, PC-based, and all-in-one solution for developing neurally inspired BMI controllers. We believe that the BNDE is the first implementation, which is capable of creating hybrid biological/in silico neural networks for motor neuroprosthetic control and utilizes multiple CPU cores for computationally intensive real-time SNN simulations. PMID:26321943

  1. In silico prediction of splice-altering single nucleotide variants in the human genome

    PubMed Central

    Jian, Xueqiu; Boerwinkle, Eric; Liu, Xiaoming

    2014-01-01

    In silico tools have been developed to predict variants that may have an impact on pre-mRNA splicing. The major limitation of the application of these tools to basic research and clinical practice is the difficulty in interpreting the output. Most tools only predict potential splice sites given a DNA sequence without measuring splicing signal changes caused by a variant. Another limitation is the lack of large-scale evaluation studies of these tools. We compared eight in silico tools on 2959 single nucleotide variants within splicing consensus regions (scSNVs) using receiver operating characteristic analysis. The Position Weight Matrix model and MaxEntScan outperformed other methods. Two ensemble learning methods, adaptive boosting and random forests, were used to construct models that take advantage of individual methods. Both models further improved prediction, with outputs of directly interpretable prediction scores. We applied our ensemble scores to scSNVs from the Catalogue of Somatic Mutations in Cancer database. Analysis showed that predicted splice-altering scSNVs are enriched in recurrent scSNVs and known cancer genes. We pre-computed our ensemble scores for all potential scSNVs across the human genome, providing a whole genome level resource for identifying splice-altering scSNVs discovered from large-scale sequencing studies. PMID:25416802

  2. Investigation of protein selectivity in multimodal chromatography using in silico designed Fab fragment variants.

    PubMed

    Karkov, Hanne Sophie; Krogh, Berit Olsen; Woo, James; Parimal, Siddharth; Ahmadian, Haleh; Cramer, Steven M

    2015-11-01

    In this study, a unique set of antibody Fab fragments was designed in silico and produced to examine the relationship between protein surface properties and selectivity in multimodal chromatographic systems. We hypothesized that multimodal ligands containing both hydrophobic and charged moieties would interact strongly with protein surface regions where charged groups and hydrophobic patches were in close spatial proximity. Protein surface property characterization tools were employed to identify the potential multimodal ligand binding regions on the Fab fragment of a humanized antibody and to evaluate the impact of mutations on surface charge and hydrophobicity. Twenty Fab variants were generated by site-directed mutagenesis, recombinant expression, and affinity purification. Column gradient experiments were carried out with the Fab variants in multimodal, cation-exchange, and hydrophobic interaction chromatographic systems. The results clearly indicated that selectivity in the multimodal system was different from the other chromatographic modes examined. Column retention data for the reduced charge Fab variants identified a binding site comprising light chain CDR1 as the main electrostatic interaction site for the multimodal and cation-exchange ligands. Furthermore, the multimodal ligand binding was enhanced by additional hydrophobic contributions as evident from the results obtained with hydrophobic Fab variants. The use of in silico protein surface property analyses combined with molecular biology techniques, protein expression, and chromatographic evaluations represents a previously undescribed and powerful approach for investigating multimodal selectivity with complex biomolecules. PMID:25950863

  3. Toward Building Hybrid Biological/in silico Neural Networks for Motor Neuroprosthetic Control.

    PubMed

    Kocaturk, Mehmet; Gulcur, Halil Ozcan; Canbeyli, Resit

    2015-01-01

    In this article, we introduce the Bioinspired Neuroprosthetic Design Environment (BNDE) as a practical platform for the development of novel brain-machine interface (BMI) controllers, which are based on spiking model neurons. We built the BNDE around a hard real-time system so that it is capable of creating simulated synapses from extracellularly recorded neurons to model neurons. In order to evaluate the practicality of the BNDE for neuroprosthetic control experiments, a novel, adaptive BMI controller was developed and tested using real-time closed-loop simulations. The present controller consists of two in silico medium spiny neurons, which receive simulated synaptic inputs from recorded motor cortical neurons. In the closed-loop simulations, the recordings from the cortical neurons were imitated using an external, hardware-based neural signal synthesizer. By implementing a reward-modulated spike timing-dependent plasticity rule, the controller achieved perfect target reach accuracy for a two-target reaching task in one-dimensional space. The BNDE combines the flexibility of software-based spiking neural network (SNN) simulations with powerful online data visualization tools and is a low-cost, PC-based, and all-in-one solution for developing neurally inspired BMI controllers. We believe that the BNDE is the first implementation, which is capable of creating hybrid biological/in silico neural networks for motor neuroprosthetic control and utilizes multiple CPU cores for computationally intensive real-time SNN simulations. PMID:26321943

  4. Scrotal Irradiation in Primary Testicular Lymphoma: Review of the Literature and In Silico Planning Comparative Study

    SciTech Connect

    Brouwer, Charlotte L.; Wiesendanger, Esther M.; Hulst, Peter C. van der; Imhoff, Gustaaf W. van; Langendijk, Johannes A.; Beijert, Max

    2013-02-01

    We examined adjuvant irradiation of the scrotum in primary testicular lymphoma (PTL) by means of a literature review in MEDLINE, a telephone survey among Dutch institutes, and an in silico planning comparative study on scrotal irradiation in PTL. We did not find any uniform adjuvant irradiation technique assuring a safe planning target volume (PTV) coverage in published reports, and the definition of the clinical target volume is unclear. Histopathologic studies of PTL show a high invasion rate of the tunica albuginea, the epididymis, and the spermatic cord. In retrospective studies, a prescribed dose of at least 30 Gy involving the scrotum is associated with best survival. The majority of Dutch institutes irradiate the whole scrotum without using a planning computed tomography scan, with a single electron beam and a total dose of 30 Gy. The in silico planning comparative study showed that all evaluated approaches met a D{sub 95%} scrotal dose of at least 85% of the prescription dose, without exceeding the dose limits of critical organs. Photon irradiation with 2 oblique beams using wedges resulted in the best PTV coverage, with a mean value of 95% of the prescribed dose, with lowest maximum dose. Adjuvant photon or electron irradiation of the whole scrotum including the contralateral testicle with a minimum dose of 30 Gy is recommended in PTL. Computed tomography-based radiation therapy treatment planning with proper patient positioning and position verification guarantees optimal dose coverage.

  5. Optimized method for TAG protein homology modeling: In silico and experimental structural characterization.

    PubMed

    Tomar, Jyoti Singh; Peddinti, Rama Krishna

    2016-07-01

    The DNA glycosylases cleave CN glycosyl bond to release a free base and generate abasic sites concurrently. Function and structure of these enzymes in the pathogenic bacterium Acinetobacter baumannii and its closely related species are not well characterized. Inhibition of TAG enzyme is a promising drug design strategy against A. baumannii. Here optimized molecular modeling approaches were used to provide a structural scaffold of TAG. The recombinant TAG protein was expressed and purified to determine oligomeric state using size exclusion chromatography, which showed the existence of TAG protein as monomer (mwt ∼21kDa). Secondary structure and substrate binding were analyzed using CD are in good agreement with the in silico predictions. Near UV-CD spectrum shows the involvement of Tyr residues in substrate recognition. Molecular docking studies were performed to understand the molecular recognition interactions and this knowledge was used to identify the potent inhibitors using virtual screening. Residues crucial for DNA holding and enzyme catalysis are reconfirmed by the in silico mutational studies. PMID:27017978

  6. Design, Fabrication and Characterization of an In Silico Cell Physiology lab for Bio Sensing Applications

    NASA Astrophysics Data System (ADS)

    Haque, A. ul; Rokkam, M.; DeCarlo, A. R.; Wereley, S. T.; Wells, H. W.; McLamb, W. T.; Roux, S. J.; Irazoqui, P. P.; Porterfield, D. M.

    2006-04-01

    In this paper, we report the design, fabrication and characterization of an In Silico cell physiology biochip for measuring Ca2+ ion concentrations and currents around single cells. This device has been designed around specific science objectives of measuring real time multidimensional calcium flux patterns around sixteen Ceratopteris richardii fern spores in microgravity flight experiments and ground studies. The sixteen microfluidic cell holding pores are 150 by 150 µm each and have 4 Ag/AgCl electrodes leading into them. An SU-8 structural layer is used for insulation and packaging purposes. The In Silico cell physiology lab is wire bonded on to a custom PCB for easy interface with a state of the art data acquisition system. The electrodes are coated with a Ca2+ ion selective membrane based on ETH-5234 ionophore and operated against an Ag/AgCl reference electrode. Initial characterization results have shown Nernst slopes of 30mv/decade that were stable over a number of measurement cycles. While this work is focused on technology to enable basic research on the Ceratopteris richardii spores, we anticipate that this type of cell physiology lab-on-a-chip will be broadly applied in biomedical and pharmacological research by making minor modifications to the electrode material and the measurement technique. Future applications include detection of glucose, hormones such as plant auxin, as well as multiple analyte detection on the same chip.

  7. In Silico Design of a Chimeric Protein Containing Antigenic Fragments of Helicobacter pylori; A Bioinformatic Approach

    PubMed Central

    Mohammad, Nazanin; Karsabet, Mehrnaz Taghipour; Amani, Jafar; Ardjmand, Abolfazl; Zadeh, Mohsen Razavi; Gholi, Mohammad Khalifeh; Saffari, Mahmood; Ghasemi, Amir

    2016-01-01

    Helicobacter pylori is a global health problem which has encouraged scientists to find new ways to diagnose, immunize and eradicate the H. pylori infection. In silico studies are a promising approach to design new chimeric antigen having the immunogenic potential of several antigens. In order to obtain such benefit in H. pylori vaccine study, a chimeric gene containing four fragments of FliD sequence (1-600 bp), UreB (327-334 bp),VacA (744-805 bp) and CagL(51-100 bp) which have a high density of B- and T-cell epitopes was designed. The secondary and tertiary structures of the chimeric protein and other properties such as stability, solubility and antigenicity were analyzed. The in silico results showed that after optimizing for the purpose of expression in Escherichia coli BL21, the solubility and antigenicity of the construct fragments were highly retained. Most regions of the chimeric protein were found to have a high antigenic propensity and surface accessibility. These results would be useful in animal model application and accounted for the development of an epitope-based vaccine against the H. pylori. PMID:27335622

  8. In-silico identification of miRNAs and their regulating target functions in Ocimum basilicum.

    PubMed

    Singh, Noopur; Sharma, Ashok

    2014-12-01

    microRNA is known to play an important role in growth and development of the plants and also in environmental stress. Ocimum basilicum (Basil) is a well known herb for its medicinal properties. In this study, we used in-silico approaches to identify miRNAs and their targets regulating different functions in O. basilicum using EST approach. Additionally, functional annotation, gene ontology and pathway analysis of identified target transcripts were also done. Seven miRNA families were identified. Meaningful regulations of target transcript by identified miRNAs were computationally evaluated. Four miRNA families have been reported by us for the first time from the Lamiaceae. Our results further confirmed that uracil was the predominant base in the first positions of identified mature miRNA sequence, while adenine and uracil were predominant in pre-miRNA sequences. Phylogenetic analysis was carried out to determine the relation between O. basilicum and other plant pre-miRNAs. Thirteen potential targets were evaluated for 4 miRNA families. Majority of the identified target transcripts regulated by miRNAs showed response to stress. miRNA 5021 was also indicated for playing an important role in the amino acid metabolism and co-factor metabolism in this plant. To the best of our knowledge this is the first in silico study describing miRNAs and their regulation in different metabolic pathways of O. basilicum. PMID:25256277

  9. DNA barcoding in plants: evolution and applications of in silico approaches and resources.

    PubMed

    Bhargava, Mili; Sharma, Ashok

    2013-06-01

    Bioinformatics has played an important role in the analysis of DNA barcoding data. The process of DNA barcoding initially involves the available data collection from the existing databases. Many databases have been developed in recent years, e.g. MMDBD [Medicinal Materials DNA Barcode Database], BioBarcode, etc. In case of non-availability of sequences, sequencing has to be done in vitro for which a recently developed software ecoPrimers can be helpful. This is followed by multiple sequence alignment. Further, basic sequence statistics computation and phylogenetic analysis can be performed by MEGA and PHYLIP/PAUP tools respectively. Some of the recent tools for in silico and statistical analysis specifically designed for barcoding viz. CAOS (Character Based DNA Barcoding), BRONX (DNA Barcode Sequence Identification Incorporating Taxonomic Hierarchy and within Taxon Variability), Spider (Analysis of species identity and evolution, particularly DNA barcoding), jMOTU and Taxonerator (Turning DNA Barcode Sequences into Annotated OTUs), OTUbase (Analysis of OTU data and taxonomic data), SAP (Statistical Assignment Package), etc. have been discussed and analysed in this review. The paper presents a comprehensive overview of the various in silico methods, tools, softwares and databases used for DNA barcoding of plants. PMID:23500333

  10. Spatio-temporal Model of Xenobiotic Distribution and Metabolism in an in Silico Mouse Liver Lobule

    NASA Astrophysics Data System (ADS)

    Fu, Xiao; Sluka, James; Clendenon, Sherry; Glazier, James; Ryan, Jennifer; Dunn, Kenneth; Wang, Zemin; Klaunig, James

    Our study aims to construct a structurally plausible in silico model of a mouse liver lobule to simulate the transport of xenobiotics and the production of their metabolites. We use a physiologically-based model to calculate blood-flow rates in a network of mouse liver sinusoids and simulate transport, uptake and biotransformation of xenobiotics within the in silico lobule. Using our base model, we then explore the effects of variations of compound-specific (diffusion, transport and metabolism) and compound-independent (temporal alteration of blood flow pattern) parameters, and examine their influence on the distribution of xenobiotics and metabolites. Our simulations show that the transport mechanism (diffusive and transporter-mediated) of xenobiotics and blood flow both impact the regional distribution of xenobiotics in a mouse hepatic lobule. Furthermore, differential expression of metabolic enzymes along each sinusoid's portal to central axis, together with differential cellular availability of xenobiotics, induce non-uniform production of metabolites. Thus, the heterogeneity of the biochemical and biophysical properties of xenobiotics, along with the complexity of blood flow, result in different exposures to xenobiotics for hepatocytes at different lobular locations. We acknowledge support from National Institute of Health GM 077138 and GM 111243.

  11. In silico analysis of Burkholderia pseudomallei genome sequence for potential drug targets.

    PubMed

    Chong, Chan-Eng; Lim, Boon-San; Nathan, Sheila; Mohamed, Rahmah

    2006-01-01

    Recent advances in DNA sequencing technology have enabled elucidation of whole genome information from a plethora of organisms. In parallel with this technology, various bioinformatics tools have driven the comparative analysis of the genome sequences between species and within isolates. While drawing meaningful conclusions from a large amount of raw material, computer-aided identification of suitable targets for further experimental analysis and characterization, has also led to the prediction of non-human homologous essential genes in bacteria as promising candidates for novel drug discovery. Here, we present a comparative genomic analysis to identify essential genes in Burkholderia pseudomallei. Our in silico prediction has identified 312 essential genes which could also be potential drug candidates. These genes encode essential proteins to support the survival of B. pseudomallei including outer-inner membrane and surface structures, regulators, proteins involved in pathogenenicity, adaptation, chaperones as well as degradation of small and macromolecules, energy metabolism, information transfer, central/intermediate/miscellaneous metabolism pathways and some conserved hypothetical proteins of unknown function. Therefore, our in silico approach has enabled rapid screening and identification of potential drug targets for further characterization in the laboratory. PMID:16922696

  12. Integration of Molecular Networking and In-Silico MS/MS Fragmentation for Natural Products Dereplication.

    PubMed

    Allard, Pierre-Marie; Péresse, Tiphaine; Bisson, Jonathan; Gindro, Katia; Marcourt, Laurence; Pham, Van Cuong; Roussi, Fanny; Litaudon, Marc; Wolfender, Jean-Luc

    2016-03-15

    Dereplication represents a key step for rapidly identifying known secondary metabolites in complex biological matrices. In this context, liquid-chromatography coupled to high resolution mass spectrometry (LC-HRMS) is increasingly used and, via untargeted data-dependent MS/MS experiments, massive amounts of detailed information on the chemical composition of crude extracts can be generated. An efficient exploitation of such data sets requires automated data treatment and access to dedicated fragmentation databases. Various novel bioinformatics approaches such as molecular networking (MN) and in-silico fragmentation tools have emerged recently and provide new perspective for early metabolite identification in natural products (NPs) research. Here we propose an innovative dereplication strategy based on the combination of MN with an extensive in-silico MS/MS fragmentation database of NPs. Using two case studies, we demonstrate that this combined approach offers a powerful tool to navigate through the chemistry of complex NPs extracts, dereplicate metabolites, and annotate analogues of database entries. PMID:26882108

  13. In silico prediction of toxic action mechanisms of phenols for imbalanced data with Random Forest learner.

    PubMed

    Chen, Jing; Tang, Yuan Yan; Fang, Bin; Guo, Chang

    2012-05-01

    With an increasing need for the rapid and effective safety assessment of compounds in industrial and civil-use products, in silico toxicity exploration techniques provide an economic way for environmental hazard assessment. The previous in silico researches have developed many quantitative structure-activity relationships models to predict toxicity mechanisms for last decade. Most of these methods benefit from data analysis and machine learning techniques, which rely heavily on the characteristics of data sets. For Tetrahymena pyriformis toxicity data sets, there is a great technical challenge-data imbalance. The skewness of data class distribution would greatly deteriorate the prediction performance on rare classes. Most of the previous researches for phenol mechanisms of toxic action prediction did not consider this practical problem. In this work, we dealt with the problem by considering the difference between the two types of misclassifications. Random Forest learner was employed in cost-sensitive learning framework to construct prediction models based on selected molecular descriptors. In computational experiments, both the global and local models obtained appreciable overall prediction accuracies. Particularly, the performance on rare classes was indeed promoted. Moreover, for practical usage of these models, the balance of the two misclassifications can be adjusted by using different cost matrices according to the application goals. PMID:22481075

  14. Small Molecule Agonists for the Type I Interferon Receptor: An In Silico Approach.

    PubMed

    Wei, Lianhu; Bello, Angelica M; Majchrzak-Kita, Beata; Salum, Noruê; Lewis, Melissa M; Kotra, Lakshmi P; Fish, Eleanor N

    2016-03-01

    Type I interferons (IFNs) exhibit broad-spectrum antiviral activity, with potential utility against emerging acute virus infections that pose a threat to global health. Recombinant IFN-αs that have been approved for clinical use require cold storage and are administered through intramuscular or subcutaneous injection, features that are problematic for global distribution, storage, and administration. Cognizant that the biological potency of an IFN-α subtype is determined by its binding affinity to the type I IFN receptor, IFNAR, we identified a panel of small molecule nonpeptide compounds using an in silico screening strategy that incorporated specific structural features of amino acids in the receptor-binding domains of the most potent IFN-α, IFN alfacon-1. Hit compounds were selected based on ease of synthesis and formulation properties. In preliminary biological assays, we provide evidence that these compounds exhibit antiviral activity. This proof-of-concept study validates the strategy of in silico design and development for IFN mimetics. PMID:26700737

  15. FutureTox II: in vitro data and in silico models for predictive toxicology.

    PubMed

    Knudsen, Thomas B; Keller, Douglas A; Sander, Miriam; Carney, Edward W; Doerrer, Nancy G; Eaton, David L; Fitzpatrick, Suzanne Compton; Hastings, Kenneth L; Mendrick, Donna L; Tice, Raymond R; Watkins, Paul B; Whelan, Maurice

    2015-02-01

    FutureTox II, a Society of Toxicology Contemporary Concepts in Toxicology workshop, was held in January, 2014. The meeting goals were to review and discuss the state of the science in toxicology in the context of implementing the NRC 21st century vision of predicting in vivo responses from in vitro and in silico data, and to define the goals for the future. Presentations and discussions were held on priority concerns such as predicting and modeling of metabolism, cell growth and differentiation, effects on sensitive subpopulations, and integrating data into risk assessment. Emerging trends in technologies such as stem cell-derived human cells, 3D organotypic culture models, mathematical modeling of cellular processes and morphogenesis, adverse outcome pathway development, and high-content imaging of in vivo systems were discussed. Although advances in moving towards an in vitro/in silico based risk assessment paradigm were apparent, knowledge gaps in these areas and limitations of technologies were identified. Specific recommendations were made for future directions and research needs in the areas of hepatotoxicity, cancer prediction, developmental toxicity, and regulatory toxicology. PMID:25628403

  16. In silico inhibition of GABARAP activity using antiepileptic medicinal derived compounds

    PubMed Central

    Mathew, Shilu; Faheem, Muhammad; Al-Malki, Abdulrahman L; Kumosani, Taha A; Qadri, Ishtiaq

    2015-01-01

    Epilepsy is a neurological disorder affecting more than 50 million people worldwide. It can be controlled by antiepileptic drugs (AEDs) but more than 30% patients are still resistant to AEDs. To overcome this problem, researchers are trying to develop novel approaches to treat epilepsy including the use of herbal medicines. The γ-amino butyric acid type-A receptor associated protein (GABARAP) is ubiquitin-like modifier implicated in the intracellular trafficking of GABAAR. An in silico mutation was created at 116 amino acid position G116A, and an in silico study was carried out to identify the potential binding inhibitors (with antiepileptic properties) against the active sites of GABARAP. Five different plant derived compounds namely (a) Aconitine (b) Berberine (c) Montanine (d) Raubasine (e) Safranal were selected, and their quantitative structure-activity relationships (QSAR) have been conducted to search the inhibitory activity of the selected compounds. The results have shown maximum number of hydrogen bond (H-bond) interactions of Raubasine with highest interaction energy among all of the five compounds. So, Raubasine could be the best fit ligand of GABARAP but in vitro, and in vivo studies are necessary for further confirmation. PMID:26124559

  17. Oleanolic acid (OA) as an antileishmanial agent: Biological evaluation and in silico mechanistic insights.

    PubMed

    Melo, Tahira Souza; Gattass, Cerli Rocha; Soares, Deivid Costa; Cunha, Micael Rodrigues; Ferreira, Christian; Tavares, Maurício Temotheo; Saraiva, Elvira; Parise-Filho, Roberto; Braden, Hannah; Delorenzi, Jan Carlo

    2016-06-01

    Although a worldwide health problem, leishmaniasis is considered a highly neglected disease, lacking efficient and low toxic treatment. The efforts for new drug development are based on alternatives such as new uses for well-known drugs, in silico and synthetic studies and naturally derived compounds. Oleanolic acid (OA) is a pentacyclic triterpenoid widely distributed throughout the Plantae kingdom that displays several pharmacological activities. OA showed potent leishmancidal effects in different Leishmania species, both against promastigotes (IC(50 L. braziliensis) 30.47 ± 6.35 μM; IC(50 L. amazonensis) 40.46 ± 14.21 μM; IC(50 L. infantum) 65.93 ± 15.12 μM) and amastigotes (IC(50 L. braziliensis) 68.75 ± 16.55 μM; IC(50 L. amazonensis) 38.45 ± 12.05 μM; IC(50 L. infantum) 64.08 ± 23.52 μM), with low cytotoxicity against mouse peritoneal macrophages (CC(50) 235.80 ± 36.95 μM). Moreover, in silico studies performed to evaluate OA molecular properties and to elucidate the possible mechanism of action over the Leishmania enzyme sterol 14α-demethylase (CYP51) suggested that OA interacts efficiently with CYP51 and could inhibit the ergosterol synthesis pathway. Collectively, these data indicate that OA is a good candidate as leading compound for the development of a new leishmaniasis treatment. PMID:26772973

  18. In-silico Metabolome Target Analysis Towards PanC-based Antimycobacterial Agent Discovery.

    PubMed

    Khoshkholgh-Sima, Baharak; Sardari, Soroush; Izadi Mobarakeh, Jalal; Khavari-Nejad, Ramezan Ali

    2015-01-01

    Mycobacterium tuberculosis, the main cause of tuberculosis (TB), has still remained a global health crisis especially in developing countries. Tuberculosis treatment is a laborious and lengthy process with high risk of noncompliance, cytotoxicity adverse events and drug resistance in patient. Recently, there has been an alarming rise of drug resistant in TB. In this regard, it is an unmet need to develop novel antitubercular medicines that target new or more effective biochemical pathways to prevent drug resistant Mycobacterium. Integrated study of metabolic pathways through in-silico approach played a key role in antimycobacterial design process in this study. Our results suggest that pantothenate synthetase (PanC), anthranilate phosphoribosyl transferase (TrpD) and 3-isopropylmalate dehydratase (LeuD) might be appropriate drug targets. In the next step, in-silico ligand analysis was used for more detailed study of chemical tractability of targets. This was helpful to identify pantothenate synthetase (PanC, Rv3602c) as the best target for antimycobacterial design procedure. Virtual library screening on the best ligand of PanC was then performed for inhibitory ligand design. At the end, five chemical intermediates showed significant inhibition of Mycobacterium bovis with good selectivity indices (SI) ≥10 according to Tuberculosis Antimicrobial Acquisition & Coordinating Facility of US criteria for antimycobacterial screening programs. PMID:25561926

  19. Improving compound quality through in vitro and in silico physicochemical profiling.

    PubMed

    van de Waterbeemd, Han

    2009-11-01

    Many compounds entering clinical studies do not survive the numerous hurdles for a good pharmacological lead to a drug on the market. The reasons for attrition have been widely studied which resulted in more early attention to compound quality related to physical chemistry, drug metabolism and pharmacokinetics (DMPK), and toxicology/safety. This paper will briefly review current physicochemical in vitro assays and in silico predictions to support compound and library design through to lead optimization. The most important physicochemical properties include lipophilicity (log P/D), pKa, solubility, and permeability. These drive key ADMET properties such as absorption, cell penetration, access to the brain, volume of distribution, plasma protein binding, metabolism, and toxicity, as well as biopharmaceutical behavior. Much data are now available from medium- to high-throughput physchem and ADMET in vitro assays, either in the public domain (see, e.g., PubChem, PubMed) or in drug companies' in-house databases. Such data are increasingly being computer-modelled and used in predictive chemistry. New pipelining technology makes it easier to build and update QSAR models so that such models can use the latest available data to produce robust local and global predictive in silico ADMET models. PMID:19937820

  20. FutureTox II: In vitro Data and In Silico Models for Predictive Toxicology

    PubMed Central

    Knudsen, Thomas B.; Keller, Douglas A.; Sander, Miriam; Carney, Edward W.; Doerrer, Nancy G.; Eaton, David L.; Fitzpatrick, Suzanne Compton; Hastings, Kenneth L.; Mendrick, Donna L.; Tice, Raymond R.; Watkins, Paul B.; Whelan, Maurice

    2015-01-01

    FutureTox II, a Society of Toxicology Contemporary Concepts in Toxicology workshop, was held in January, 2014. The meeting goals were to review and discuss the state of the science in toxicology in the context of implementing the NRC 21st century vision of predicting in vivo responses from in vitro and in silico data, and to define the goals for the future. Presentations and discussions were held on priority concerns such as predicting and modeling of metabolism, cell growth and differentiation, effects on sensitive subpopulations, and integrating data into risk assessment. Emerging trends in technologies such as stem cell-derived human cells, 3D organotypic culture models, mathematical modeling of cellular processes and morphogenesis, adverse outcome pathway development, and high-content imaging of in vivo systems were discussed. Although advances in moving towards an in vitro/in silico based risk assessment paradigm were apparent, knowledge gaps in these areas and limitations of technologies were identified. Specific recommendations were made for future directions and research needs in the areas of hepatotoxicity, cancer prediction, developmental toxicity, and regulatory toxicology. PMID:25628403

  1. Enhancement of acetoin production in Candida glabrata by in silico-aided metabolic engineering

    PubMed Central

    2014-01-01

    Background Acetoin is a promising chemical compound that can potentially serve as a high value-added platform for a broad range of applications. Many industrial biotechnological processes are moving towards the use of yeast as a platform. The multi-auxotrophic yeast, Candida glabrata, can accumulate a large amount of pyruvate, but produces only trace amounts of acetoin. Here, we attempted to engineer C. glabrata to redirect the carbon flux of pyruvate to increase acetoin production. Results Based on an in silico strategy, a synthetic, composite metabolic pathway involving two distinct enzymes, acetolactate synthase (ALS) and acetolactate decarboxylase (ALDC), was constructed, leading to the accumulation of acetoin in C. glabrata. Further genetic modifications were introduced to increase the carbon flux of the heterologous pathway, increasing the production of acetoin to 2.08 g/L. Additionally, nicotinic acid was employed to regulate the intracellular NADH level, and a higher production of acetoin (3.67 g/L) was obtained at the expense of 2,3-butanediol production under conditions of a lower NADH/NAD+ ratio. Conclusion With the aid of in silico metabolic engineering and cofactor engineering, C. glabrata was designed and constructed to improve acetoin production. PMID:24725668

  2. Methylerythritol phosphate pathway to isoprenoids: kinetic modeling and in silico enzyme inhibitions in Plasmodium falciparum.

    PubMed

    Singh, Vivek Kumar; Ghosh, Indira

    2013-09-01

    The methylerythritol phosphate (MEP) pathway of Plasmodium falciparum (P. falciparum) has become an attractive target for anti-malarial drug discovery. This study describes a kinetic model of this pathway, its use in validating 1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR) as drug target from the systemic perspective, and additional target identification, using metabolic control analysis and in silico inhibition studies. In addition to DXR, 1-deoxy-d-xylulose 5-phosphate synthase (DXS) can be targeted because it is the first enzyme of the pathway and has the highest flux control coefficient followed by that of DXR. In silico inhibition of both enzymes caused large decrement in the pathway flux. An added advantage of targeting DXS is its influence on vitamin B1 and B6 biosynthesis. Two more potential targets, 2-C-methyl-d-erythritol 2,4-cyclodiphosphate synthase and 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase, were also identified. Their inhibition caused large accumulation of their substrates causing instability of the system. This study demonstrates that both types of enzyme targets, one acting via flux reduction and the other by metabolite accumulation, exist in P. falciparum MEP pathway. These groups of targets can be exploited for independent anti-malarial drugs. PMID:23816706

  3. Reversible nanodiamond-carbon onion phase transformations.

    PubMed

    Xiao, J; Ouyang, G; Liu, P; Wang, C X; Yang, G W

    2014-06-11

    Because of their considerable science and technical interest, nanodiamonds (3-5 nm) are often used as a model to study the phase transformation between graphite and diamond. Here we demonstrated that a reversible nanodiamond-carbon onion phase transformation can become true when laser irradiates colloidal suspensions of nanodiamonds at the ambient temperature and pressure. Nanodiamonds are first transformed to carbon onions driven by the laser-induced high temperature in which an intermediary bucky diamond phase is observed. Sequentially, carbon onions are transformed back to nanodiamonds driven by the laser-induced high temperature and high pressure from carbon onions as nanoscaled temperature and pressure cell upon the laser irradiation process in liquid. Similarly, the same bucky diamond phase serving as an intermediate phase is found during the carbon onion-to-nanodiamond transition. To have a clear insight into the unique phase transformation the thermodynamic approaches on the nanoscale were proposed to elucidate the reversible phase transformation of nanodiamond-to-carbon onion-to-nanodiamond via an intermediary bucky diamond phase upon the laser irradiation in liquid. This reversible transition reveals a series of phase transformations between diamond and carbon allotropes, such as carbon onion and bucky diamond, having a general insight into the basic physics involved in these phase transformations. These results give a clue to the root of meteoritic nanodiamonds that are commonly found in primitive meteorites but their origin is puzzling and offers one suitable approach for breaking controllable pathways between diamond and carbon allotropes. PMID:24823241

  4. Isolation, structural characterization and in silico drug-like properties prediction of a natural compound from the ethanolic extract of Cayratia trifolia (L.)

    PubMed Central

    Perumal, Palanisamy Chella; Sowmya, Sundaram; Pratibha, Prabhakaran; Vidya, Balasubramanian; Anusooriya, Palanirajan; Starlin, Thangarajan; Ravi, Subban; Gopalakrishnan, Velliyur Kanniappan

    2015-01-01

    Background: Natural products have continually played an important role in drug discovery because it serves as active principles in drugs as well as templates for synthesis of new drugs. Cayratia trifolia (L.) is a medicinal plant, which has been reported to have antiviral, antibacterial, antiprotozoal, hypoglycemic, anticancer and diuretic activities. Objective: Therefore, the objective of this study is to isolate and identify the natural compound from the ethanolic extract of Cayratia trifolia (L.) and to predict the Absorption, Distribution, Metabolism and Excretion (ADME) properties of isolated natural compound. Materials and Methods: Column chromatography and thin layer chromatography were used to isolate the natural compound and Fourier-transform infrared (FTIR) spectroscopy was used to predict the functional groups present in the isolated natural compound. The structural characterization studies were functionally carried out using 1H, 13C, two-dimensional nuclear magnetic resonance (NMR) and mass spectrometry methods. Results: FTIR showed that, the groups of OH, C-H, C = C may be present in the isolated natural compound. 1H, 13C, two-dimensional NMR and mass spectrometry data suggests that the isolated natural compound probably like linoleic acid. In silico ADME properties, prediction of the compound was under acceptable range. Conclusion: Based on the results, it can be concluded that, the isolated natural compound of linoleic acid that has been exhibited good medicinal properties. PMID:25598646

  5. Clinical, cytogenetic and molecular analysis of androgen insensitivity syndromes from south Indian cohort and detection and in-silico characterization of androgen receptor gene mutations.

    PubMed

    V G, Abilash; S, Radha; K M, Marimuthu; K, Thangaraj; S, Arun; S, Nishu; A, Mohana Priya; J, Meena; D, Anuradha

    2016-01-30

    Rare cases of 9 complete androgen insensitivity syndromes, 9 cases of partial androgen insensitivity syndromes and equal number of male control samples were selected for this study. Few strong variations in clinical features were noticed; Giemsa banded metaphase revealed a 46,XY karyotype and the frequency of chromosome aberrations were significantly higher when compared with control samples. DNA sequence analysis of the androgen receptor gene of androgen insensitivity syndromes revealed three missense mutations - c.C1713>G resulting in the replacement of a highly conserved histidine residue with glutamine p.(His571Glu) in DNA-binding domain, c.A1715>G resulting in the replacement of a highly conserved tyrosine residue with cysteine p.(Tyr572Cys) in DNA-binding domain and c.G2599>A resulting in the replacement of a highly conserved valine residue with methionine p.(Val867Met) in ligand-binding domain of androgen receptor gene respectively. The heterozygous type of mutations c.C1713>G and c.G2599>A observed in mothers of the patients for familial cases concluding that the mutation was inherited from the mother. The novel mutation c.C1713>G is reported first time in androgen insensitivity syndrome. In-silico analysis of mutations observed in androgen receptor gene of androgen insensitivity syndrome predicted that the substitution at Y572C and V867M could probably disrupt the protein structure and function. PMID:26688387

  6. Catalytic coherence transformations

    NASA Astrophysics Data System (ADS)

    Bu, Kaifeng; Singh, Uttam; Wu, Junde

    2016-04-01

    Catalytic coherence transformations allow the otherwise impossible state transformations using only incoherent operations with the aid of an auxiliary system with finite coherence that is not being consumed in any way. Here we find the necessary and sufficient conditions for the deterministic and stochastic catalytic coherence transformations between a pair of pure quantum states. In particular, we show that the simultaneous decrease of a family of Rényi entropies of the diagonal parts of the states under consideration is a necessary and sufficient condition for the deterministic catalytic coherence transformations. Similarly, for stochastic catalytic coherence transformations we find the necessary and sufficient conditions for achieving a higher optimal probability of conversion. We thus completely characterize the coherence transformations among pure quantum states under incoherent operations. We give numerous examples to elaborate our results. We also explore the possibility of the same system acting as a catalyst for itself and find that indeed self-catalysis is possible. Further, for the cases where no catalytic coherence transformation is possible we provide entanglement-assisted coherence transformations and find the necessary and sufficient conditions for such transformations.

  7. Magnetically Controlled Variable Transformer

    NASA Technical Reports Server (NTRS)

    Kleiner, Charles T.

    1994-01-01

    Improved variable-transformer circuit, output voltage and current of which controlled by use of relatively small current supplied at relatively low power to control windings on its magnetic cores. Transformer circuits of this type called "magnetic amplifiers" because ratio between controlled output power and power driving control current of such circuit large. This ratio - power gain - can be as large as 100 in present circuit. Variable-transformer circuit offers advantages of efficiency, safety, and controllability over some prior variable-transformer circuits.

  8. Endothelial repair process and its relevance to longitudinal neointimal tissue patterns: comparing histology with in silico modelling

    PubMed Central

    Tahir, Hannan; Bona-Casas, Carles; Narracott, Andrew James; Iqbal, Javaid; Gunn, Julian; Lawford, Patricia; Hoekstra, Alfons G.

    2014-01-01

    Re-establishing a functional endothelium following endovascular treatment is an important factor in arresting neointimal proliferation. In this study, both histology (in vivo) and computational simulations (in silico) are used to evaluate neointimal growth patterns within coronary arteries along the axial direction of the stent. Comparison of the growth configurations in vivo and in silico was undertaken to identify candidate mechanisms for endothelial repair. Stent, lumen and neointimal areas were measured from histological sections obtained from eight right coronary stented porcine arteries. Two re-endothelialization scenarios (endothelial cell (EC) random seeding and EC growth from proximal and distal ends) were implemented in silico to evaluate their influence on the morphology of the simulated lesions. Subject to the assumptions made in the current simulations, comparison between in vivo and in silico results suggests that endothelial growth does not occur from the proximal and distal ends alone, but is more consistent with the assumption of a random seeding process. This may occur either from the patches of endothelium which survive following stent implantation or from attachment of circulating endothelial progenitor cells. PMID:24621816

  9. Supercoiling transformation of chemical gels.

    PubMed

    Asai, Makoto; Katashima, Takuya; Sakai, Takamasa; Shibayama, Mitsuhiro

    2015-09-28

    The swelling/deswelling behavior of chemical gels has been an unsolved problem disputed over for a long time. The Obukhov-Rubinstein-Colby model depicts the influence that swelling/deswelling has on elasticity, but its physical picture is too complicated to be sufficiently validated by experiment. In this study, we use molecular dynamics simulation to verify the validity of the molecular picture of network strands predicted by the Obukhov-Rubinstein-Colby model. We conclude that the physical picture of the Obukhov-Rubinstein-Colby model is reasonable, and furthermore the simulation can reveal the details of conformational changes in network strands during the supercoiling transformation. Our findings not only reveal the validity, but also give a better understanding of the dynamics of the swelling/deswelling behavior of chemical gels. PMID:26279149

  10. In Silico Modeling of Gastrointestinal Drug Absorption: Predictive Performance of Three Physiologically Based Absorption Models.

    PubMed

    Sjögren, Erik; Thörn, Helena; Tannergren, Christer

    2016-06-01

    Gastrointestinal (GI) drug absorption is a complex process determined by formulation, physicochemical and biopharmaceutical factors, and GI physiology. Physiologically based in silico absorption models have emerged as a widely used and promising supplement to traditional in vitro assays and preclinical in vivo studies. However, there remains a lack of comparative studies between different models. The aim of this study was to explore the strengths and limitations of the in silico absorption models Simcyp 13.1, GastroPlus 8.0, and GI-Sim 4.1, with respect to their performance in predicting human intestinal drug absorption. This was achieved by adopting an a priori modeling approach and using well-defined input data for 12 drugs associated with incomplete GI absorption and related challenges in predicting the extent of absorption. This approach better mimics the real situation during formulation development where predictive in silico models would be beneficial. Plasma concentration-time profiles for 44 oral drug administrations were calculated by convolution of model-predicted absorption-time profiles and reported pharmacokinetic parameters. Model performance was evaluated by comparing the predicted plasma concentration-time profiles, Cmax, tmax, and exposure (AUC) with observations from clinical studies. The overall prediction accuracies for AUC, given as the absolute average fold error (AAFE) values, were 2.2, 1.6, and 1.3 for Simcyp, GastroPlus, and GI-Sim, respectively. The corresponding AAFE values for Cmax were 2.2, 1.6, and 1.3, respectively, and those for tmax were 1.7, 1.5, and 1.4, respectively. Simcyp was associated with underprediction of AUC and Cmax; the accuracy decreased with decreasing predicted fabs. A tendency for underprediction was also observed for GastroPlus, but there was no correlation with predicted fabs. There were no obvious trends for over- or underprediction for GI-Sim. The models performed similarly in capturing dependencies on dose and

  11. In-silico predictive mutagenicity model generation using supervised learning approaches

    PubMed Central

    2012-01-01

    Background Experimental screening of chemical compounds for biological activity is a time consuming and expensive practice. In silico predictive models permit inexpensive, rapid “virtual screening” to prioritize selection of compounds for experimental testing. Both experimental and in silico screening can be used to test compounds for desirable or undesirable properties. Prior work on prediction of mutagenicity has primarily involved identification of toxicophores rather than whole-molecule predictive models. In this work, we examined a range of in silico predictive classification models for prediction of mutagenic properties of compounds, including methods such as J48 and SMO which have not previously been widely applied in cheminformatics. Results The Bursi mutagenicity data set containing 4337 compounds (Set 1) and a Benchmark data set of 6512 compounds (Set 2) were taken as input data set in this work. A third data set (Set 3) was prepared by joining up the previous two sets. Classification algorithms including Naïve Bayes, Random Forest, J48 and SMO with 10 fold cross-validation and default parameters were used for model generation on these data sets. Models built using the combined performed better than those developed from the Benchmark data set. Significantly, Random Forest outperformed other classifiers for all the data sets, especially for Set 3 with 89.27% accuracy, 89% precision and ROC of 95.3%. To validate the developed models two external data sets, AID1189 and AID1194, with mutagenicity data were tested showing 62% accuracy with 67% precision and 65% ROC area and 91% accuracy, 91% precision with 96.3% ROC area respectively. A Random Forest model was used on approved drugs from DrugBank and metabolites from the Zinc Database with True Positives rate almost 85% showing the robustness of the model. Conclusion We have created a new mutagenicity benchmark data set with around 8,000 compounds. Our work shows that highly accurate predictive

  12. In vivo and in silico determination of essential genes of Campylobacter jejuni

    PubMed Central

    2011-01-01

    Background In the United Kingdom, the thermophilic Campylobacter species C. jejuni and C. coli are the most frequent causes of food-borne gastroenteritis in humans. While campylobacteriosis is usually a relatively mild infection, it has a significant public health and economic impact, and possible complications include reactive arthritis and the autoimmune diseases Guillain-Barré syndrome. The rapid developments in "omics" technologies have resulted in the availability of diverse datasets allowing predictions of metabolism and physiology of pathogenic micro-organisms. When combined, these datasets may allow for the identification of potential weaknesses that can be used for development of new antimicrobials to reduce or eliminate C. jejuni and C. coli from the food chain. Results A metabolic model of C. jejuni was constructed using the annotation of the NCTC 11168 genome sequence, a published model of the related bacterium Helicobacter pylori, and extensive literature mining. Using this model, we have used in silico Flux Balance Analysis (FBA) to determine key metabolic routes that are essential for generating energy and biomass, thus creating a list of genes potentially essential for growth under laboratory conditions. To complement this in silico approach, candidate essential genes have been determined using a whole genome transposon mutagenesis method. FBA and transposon mutagenesis (both this study and a published study) predict a similar number of essential genes (around 200). The analysis of the intersection between the three approaches highlights the shikimate pathway where genes are predicted to be essential by one or more method, and tend to be network hubs, based on a previously published Campylobacter protein-protein interaction network, and could therefore be targets for novel antimicrobial therapy. Conclusions We have constructed the first curated metabolic model for the food-borne pathogen Campylobacter jejuni and have presented the resulting

  13. Nonlinear Bogolyubov-Valatin transformations: Two modes

    SciTech Connect

    Scharnhorst, K.; Holten, J.-W. van

    2011-11-15

    Extending our earlier study of nonlinear Bogolyubov-Valatin transformations (canonical transformations for fermions) for one fermionic mode, in the present paper, we perform a thorough study of general (nonlinear) canonical transformations for two fermionic modes. We find that the Bogolyubov-Valatin group for n=2 fermionic modes, which can be implemented by means of unitary SU(2{sup n}=4) transformations, is isomorphic to SO(6;R)/Z{sub 2}. The investigation touches on a number of subjects. As a novelty from a mathematical point of view, we study the structure of nonlinear basis transformations in a Clifford algebra [specifically, in the Clifford algebra C(0,4)] entailing (supersymmetric) transformations among multivectors of different grades. A prominent algebraic role in this context is being played by biparavectors (linear combinations of products of Dirac matrices, quadriquaternions, sedenions) and spin bivectors (antisymmetric complex matrices). The studied biparavectors are equivalent to Eddington's E-numbers and can be understood in terms of the tensor product of two commuting copies of the division algebra of quaternions H. From a physical point of view, we present a method to diagonalize any arbitrary two-fermion Hamiltonians. Relying on Jordan-Wigner transformations for two-spin-1/2 and single-spin-3/2 systems, we also study nonlinear spin transformations and the related problem of diagonalizing arbitrary two-spin-1/2 and single-spin-3/2 Hamiltonians. Finally, from a calculational point of view, we pay due attention to explicit parametrizations of SU(4) and SO(6;R) matrices (of respective sizes 4x4 and 6x6) and their mutual relation. - Highlights: > Reveals the structure of nonlinear canonical transformations for two fermionic modes. > Studies nonlinear basis transformations in a Clifford algebra. > Focuses on methodological and structural aspects. > Presents a new approach to the diagonalization of 4x4 matrix Hamiltonians. > Presents the relation between

  14. Structural transformation in monolayer materials: a 2D to 1D transformation.

    PubMed

    Momeni, Kasra; Attariani, Hamed; LeSar, Richard A

    2016-07-20

    Reducing the dimensions of materials to atomic scales results in a large portion of atoms being at or near the surface, with lower bond order and thus higher energy. At such scales, reduction of the surface energy and surface stresses can be the driving force for the formation of new low-dimensional nanostructures, and may be exhibited through surface relaxation and/or surface reconstruction, which can be utilized for tailoring the properties and phase transformation of nanomaterials without applying any external load. Here we used atomistic simulations and revealed an intrinsic structural transformation in monolayer materials that lowers their dimension from 2D nanosheets to 1D nanostructures to reduce their surface and elastic energies. Experimental evidence of such transformation has also been revealed for one of the predicted nanostructures. Such transformation plays an important role in bi-/multi-layer 2D materials. PMID:27388501

  15. In silico regenerative medicine: how computational tools allow regulatory and financial challenges to be addressed in a volatile market

    PubMed Central

    Geris, L.; Guyot, Y.; Schrooten, J.; Papantoniou, I.

    2016-01-01

    The cell therapy market is a highly volatile one, due to the use of disruptive technologies, the current economic situation and the small size of the market. In such a market, companies as well as academic research institutes are in need of tools to advance their understanding and, at the same time, reduce their R&D costs, increase product quality and productivity, and reduce the time to market. An additional difficulty is the regulatory path that needs to be followed, which is challenging in the case of cell-based therapeutic products and should rely on the implementation of quality by design (QbD) principles. In silico modelling is a tool that allows the above-mentioned challenges to be addressed in the field of regenerative medicine. This review discusses such in silico models and focuses more specifically on the bioprocess. Three (clusters of) examples related to this subject are discussed. The first example comes from the pharmaceutical engineering field where QbD principles and their implementation through the use of in silico models are both a regulatory and economic necessity. The second example is related to the production of red blood cells. The described in silico model is mainly used to investigate the manufacturing process of the cell-therapeutic product, and pays special attention to the economic viability of the process. Finally, we describe the set-up of a model capturing essential events in the development of a tissue-engineered combination product in the context of bone tissue engineering. For each of the examples, a short introduction to some economic aspects is given, followed by a description of the in silico tool or tools that have been developed to allow the implementation of QbD principles and optimal design. PMID:27051516

  16. In Silico analysis of perturbed steroidogenesis and gonad growth in fathead minnows (P. promelas) exposed to 17α-ethynylestradiol.

    PubMed

    Hala, David; Petersen, Lene H; Martinović, Dalma; Huggett, Duane B

    2015-06-01

    The multi-factorial nature of adverse reproductive effects mediated by endocrine disrupting compounds (or EDCs) makes understanding the mechanistic basis of reproductive dysfunction a highly pertinent area of research. As a consequence, a main motivator for continued research is to integrate 'multi-leveled' complexity (i.e., from genes to phenotype) using mathematical methods capable of encapsulating properties of physiological relevance. In this study, an in silico stoichiometric model of piscine steroidogenesis was augmented with a 'biomass' reaction associating the underlying stoichiometry of steroidogenesis with a reaction representative of gonad growth. The ability of the in silico model to predict perturbed steroidogenesis and subsequent effects on gonad growth was tested by exposing reproductively active male and female fathead minnows (Pimephales promelas) to 88 ng/L of the synthetic estrogen, 17α-ethynylestradiol (EE2). The in silico model was parameterized (or constrained) with experimentally quantified concentrations of selected steroid hormones (using mass spectrometry) and fold changes in gene expression (using RT-qPCR) for selected steroidogenic enzyme genes, in gonads of male and female fish. Once constrained, the optimization framework of flux balance analysis (FBA) was used to calculate an optimal flux through the biomass reaction (analogous to gonad growth) and associated steroidogenic flux distributions required to generate biomass. FBA successfully predicted effects of EE2 exposure on fathead minnow gonad growth (%gonadosomatic index or %GSI) and perturbed production of steroid hormones. Specifically, FBA accurately predicted no effects of exposure on male %GSI and a significant reduction for female %GSI. Furthermore, in silico simulations accurately identified disrupted reaction fluxes catalyzing productions of androgens (in male fish) and progestogens (in female fish), an observation which agreed with in vivo experimentation. The analyses

  17. In silico regenerative medicine: how computational tools allow regulatory and financial challenges to be addressed in a volatile market.

    PubMed

    Geris, L; Guyot, Y; Schrooten, J; Papantoniou, I

    2016-04-01

    The cell therapy market is a highly volatile one, due to the use of disruptive technologies, the current economic situation and the small size of the market. In such a market, companies as well as academic research institutes are in need of tools to advance their understanding and, at the same time, reduce their R&D costs, increase product quality and productivity, and reduce the time to market. An additional difficulty is the regulatory path that needs to be followed, which is challenging in the case of cell-based therapeutic products and should rely on the implementation of quality by design (QbD) principles. In silico modelling is a tool that allows the above-mentioned challenges to be addressed in the field of regenerative medicine. This review discusses such in silico models and focuses more specifically on the bioprocess. Three (clusters of) examples related to this subject are discussed. The first example comes from the pharmaceutical engineering field where QbD principles and their implementation through the use of in silico models are both a regulatory and economic necessity. The second example is related to the production of red blood cells. The described in silico model is mainly used to investigate the manufacturing process of the cell-therapeutic product, and pays special attention to the economic viability of the process. Finally, we describe the set-up of a model capturing essential events in the development of a tissue-engineered combination product in the context of bone tissue engineering. For each of the examples, a short introduction to some economic aspects is given, followed by a description of the in silico tool or tools that have been developed to allow the implementation of QbD principles and optimal design. PMID:27051516

  18. Chronic occupational exposure to arsenic induces carcinogenic gene signaling networks and neoplastic transformation in human lung epithelial cells

    SciTech Connect

    Stueckle, Todd A.; Lu, Yongju; Davis, Mary E.; Wang, Liying; Jiang, Bing-Hua; Holaskova, Ida; Schafer, Rosana; Barnett, John B.; Rojanasakul, Yon

    2012-06-01

    Chronic arsenic exposure remains a human health risk; however a clear mode of action to understand gene signaling-driven arsenic carcinogenesis is currently lacking. This study chronically exposed human lung epithelial BEAS-2B cells to low-dose arsenic trioxide to elucidate cancer promoting gene signaling networks associated with arsenic-transformed (B-As) cells. Following a 6 month exposure, exposed cells were assessed for enhanced cell proliferation, colony formation, invasion ability and in vivo tumor formation compared to control cell lines. Collected mRNA was subjected to whole genome expression microarray profiling followed by in silico Ingenuity Pathway Analysis (IPA) to identify lung carcinogenesis modes of action. B-As cells displayed significant increases in proliferation, colony formation and invasion ability compared to BEAS-2B cells. B-As injections into nude mice resulted in development of primary and secondary metastatic tumors. Arsenic exposure resulted in widespread up-regulation of genes associated with mitochondrial metabolism and increased reactive oxygen species protection suggesting mitochondrial dysfunction. Carcinogenic initiation via reactive oxygen species and epigenetic mechanisms was further supported by altered DNA repair, histone, and ROS-sensitive signaling. NF-κB, MAPK and NCOR1 signaling disrupted PPARα/δ-mediated lipid homeostasis. A ‘pro-cancer’ gene signaling network identified increased survival, proliferation, inflammation, metabolism, anti-apoptosis and mobility signaling. IPA-ranked signaling networks identified altered p21, EF1α, Akt, MAPK, and NF-κB signaling networks promoting genetic disorder, altered cell cycle, cancer and changes in nucleic acid and energy metabolism. In conclusion, transformed B-As cells with their whole genome expression profile provide an in vitro arsenic model for future lung cancer signaling research and data for chronic arsenic exposure risk assessment. Highlights: ► Chronic As{sub 2}O

  19. STEM Career Changers' Transformation into Science Teachers

    NASA Astrophysics Data System (ADS)

    Snyder, Catherine; Oliveira, Alandeom W.; Paska, Lawrence M.

    2013-06-01

    This study examines the transformation (professional growth) of career-changing women scientists who decided to become teachers. Drawing upon Mezirow's Transformative Learning Theory, we tracked their transformation for 3 years. Our findings revealed multiple identities, disorientation, a perceived sense of meaninglessness, loss and eventual regain in confidence, gain in pedagogical knowledge and skill, and changed perceptions of the social roles of science teachers and scientists. Driven by personal choice or need (financial, intellectual), such transformations were achieved through active pursuit of meaning in one's work, critical assessment of assumptions, planning, and trying on the unfamiliar role of a science teacher. It is argued that such transition entails complex changes in thinking about science teaching and identifying oneself as a science teacher.

  20. Transformer design tradeoffs

    NASA Technical Reports Server (NTRS)

    Mclyman, W. T.

    1977-01-01

    Technical memorandum includes transformer area product numbers, which are used to summarize dimensional and electrical properties of C-cores, pot cores, lamination, powder cores, and tape-wound cores. To aid in core selection, comparison of five common core materials is presented to indicate their influence on overall transformer efficiency and weight.

  1. Biochemical transformation of coals

    DOEpatents

    Lin, M.S.; Premuzic, E.T.

    1999-03-23

    A method of biochemically transforming macromolecular compounds found in solid carbonaceous materials, such as coal is provided. The preparation of new microorganisms, metabolically weaned through challenge growth processes to biochemically transform solid carbonaceous materials at extreme temperatures, pressures, pH, salt and toxic metal concentrations is also disclosed. 7 figs.

  2. Fourier Transform Spectrometer

    NASA Technical Reports Server (NTRS)

    1998-01-01

    Understanding the global atmospheric changes is difficult with today's current technology. However, with high resolution and nearly continuous observations from a satellite, it's possible to transform our understanding of the atmosphere. To enable the next generation of atmospheric science, a new class of orbiting atmospheric sensors is being developed. The foundation of this advanced concept is the Fourier Transform Spectrometer, or FTS.

  3. Deployment & Market Transformation (Brochure)

    SciTech Connect

    Not Available

    2012-04-01

    NREL's deployment and market transformation (D and MT) activities encompass the laboratory's full range of technologies, which span the energy efficiency and renewable energy spectrum. NREL staff educates partners on how they can advance sustainable energy applications and also provides clients with best practices for reducing barriers to innovation and market transformation.

  4. Genetic Transformation of Bacteria.

    ERIC Educational Resources Information Center

    Moss, Robert.

    1991-01-01

    An activity in which students transform an ampicillin-sensitive strain of E. coli with a plasmid containing a gene for ampicillin resistance is described. The procedure for the preparation of competent cells and the transformation of competent E. coli is provided. (KR)

  5. Support Principals, Transform Schools

    ERIC Educational Resources Information Center

    Aguilar, Elena; Goldwasser, Davina; Tank-Crestetto, Kristina

    2011-01-01

    The Transformational Coaching Team in Oakland Unified School District provides differentiated, sustained, job-embedded support to the district's school leaders. In this article, members of the team describe how they work with principals to transform the culture of schools. Student achievement data show above-average improvement in schools in which…

  6. Two Different Squeeze Transformations

    NASA Technical Reports Server (NTRS)

    Han, D. (Editor); Kim, Y. S.

    1996-01-01

    Lorentz boosts are squeeze transformations. While these transformations are similar to those in squeezed states of light, they are fundamentally different from both physical and mathematical points of view. The difference is illustrated in terms of two coupled harmonic oscillators, and in terms of the covariant harmonic oscillator formalism.

  7. A Transformation Called "Twist"

    ERIC Educational Resources Information Center

    Hwang, Daniel

    2010-01-01

    The transformations found in secondary mathematics curriculum are typically limited to stretches and translations (e.g., ACARA, 2010). Advanced students may find the transformation, twist, to be of further interest. As most available resources are written for professional-level readers, this article is intended to be an introduction accessible to…

  8. Disc piezoelectric ceramic transformers.

    PubMed

    Erhart, Jirií; Půlpán, Petr; Doleček, Roman; Psota, Pavel; Lédl, Vít

    2013-08-01

    In this contribution, we present our study on disc-shaped and homogeneously poled piezoelectric ceramic transformers working in planar-extensional vibration modes. Transformers are designed with electrodes divided into wedge, axisymmetrical ring-dot, moonie, smile, or yin-yang segments. Transformation ratio, efficiency, and input and output impedances were measured for low-power signals. Transformer efficiency and transformation ratio were measured as a function of frequency and impedance load in the secondary circuit. Optimum impedance for the maximum efficiency has been found. Maximum efficiency and no-load transformation ratio can reach almost 100% and 52 for the fundamental resonance of ring-dot transformers and 98% and 67 for the second resonance of 2-segment wedge transformers. Maximum efficiency was reached at optimum impedance, which is in the range from 500 Ω to 10 kΩ, depending on the electrode pattern and size. Fundamental vibration mode and its overtones were further studied using frequency-modulated digital holographic interferometry and by the finite element method. Complementary information has been obtained by the infrared camera visualization of surface temperature profiles at higher driving power. PMID:25004532

  9. Transformative Learning and Identity

    ERIC Educational Resources Information Center

    Illeris, Knud

    2014-01-01

    Transformative learning has usually been defined as transformations of meaning perspectives, frames of reference, and habits of mind--as proposed initially by Jack Mezirow. However, several authors have found this definition too narrow and too cognitively oriented, and Mezirow has later emphasized that emotional and social conditions are also…

  10. Adaptive Wavelet Transforms

    SciTech Connect

    Szu, H.; Hsu, C.

    1996-12-31

    Human sensors systems (HSS) may be approximately described as an adaptive or self-learning version of the Wavelet Transforms (WT) that are capable to learn from several input-output associative pairs of suitable transform mother wavelets. Such an Adaptive WT (AWT) is a redundant combination of mother wavelets to either represent or classify inputs.

  11. Direct current transformer

    NASA Technical Reports Server (NTRS)

    Khanna, S. M.; Urban, E. W. (Inventor)

    1979-01-01

    A direct current transformer in which the primary consists of an elongated strip of superconductive material, across the ends of which is direct current potential is described. Parallel and closely spaced to the primary is positioned a transformer secondary consisting of a thin strip of magnetoresistive material.

  12. Outdoor Leaders' Emotional Intelligence and Transformational Leadership

    ERIC Educational Resources Information Center

    Hayashi, Aya; Ewert, Alan

    2006-01-01

    This study explored the concept of outdoor leadership from the perspectives of emotional intelligence and transformational leadership. Levels of emotional intelligence, multifactor leadership, outdoor experience, and social desirability were examined using 46 individuals designated as outdoor leaders. The results revealed a number of unique…

  13. Positive Emotions: Passionate Scholarship and Student Transformation

    ERIC Educational Resources Information Center

    Beard, Colin; Humberstone, Barbara; Clayton, Ben

    2014-01-01

    This paper challenges the practical and conceptual understanding of the role of emotions in higher education from the twin perspectives of transition and transformation. Focusing on the neglected area of positive emotions, exploratory data reveal a rich, low-level milieu of undergraduate emotional awareness in students chiefly attributed to…

  14. A Vision for Tomorrow: Transformational Nursing Leaders.

    ERIC Educational Resources Information Center

    Ward, Kelley

    2002-01-01

    Interviews with eight transformational nursing leaders revealed that all strive for excellence, value integrity, shape their environment for success, demonstrate perseverance, attempt to improve the lives of others, possess a genuine love for people, motivate others, invent the future, and share the path toward self-discovery. (Contains 24…

  15. In silico reconstruction of the viral evolutionary lineage yields a potent gene therapy vector

    PubMed Central

    Zinn, Eric; Pacouret, Simon; Khaychuk, Vadim; Turunen, Heikki T.; Carvalho, Livia S.; Andres-Mateos, Eva; Shah, Samiksha; Shelke, Rajani; Maurer, Anna C.; Plovie, Eva; Xiao, Ru; Vandenberghe, Luk H.

    2015-01-01

    SUMMARY Adeno-associated viral vectors (AAV) have emerged as a gene delivery platform with demonstrated safety and efficacy in a handful of clinical trials for monogenic disorders. However, limitations of the current generation vectors often prevent broader application of AAV gene therapy. Efforts to engineer AAV have been hampered by a limited understanding of the structure-function relationship of the complex multimeric icosahedral architecture of the particle. To develop additional reagents pertinent to further our insight into AAV, we inferred evolutionary intermediates of the viral capsid using ancestral sequence reconstruction. In silico derived sequences were synthesized de novo and characterized for biological properties relevant to clinical applications. This effort led to the generation of 9 functional putative ancestral AAVs and the identification of Anc80, the predicted ancestor of the widely studied AAV serotypes 1, 2, 8 and 9 as a highly potent in vivo gene therapy vector for targeting liver, muscle, and retina. PMID:26235624

  16. SERAPhiC: a benchmark for in silico fragment-based drug design.

    PubMed

    Favia, Angelo D; Bottegoni, Giovanni; Nobeli, Irene; Bisignano, Paola; Cavalli, Andrea

    2011-11-28

    Our main objective was to compile a data set of high-quality protein-fragment complexes and make it publicly available. Once assembled, the data set was challenged using docking procedures to address the following questions: (i) Can molecular docking correctly reproduce the experimentally solved structures? (ii) How thorough must the sampling be to replicate the experimental data? (iii) Can commonly used scoring functions discriminate between the native pose and other energy minima? The data set, named SERAPhiC (Selected Fragment Protein Complexes), is publicly available in a ready-to-dock format ( http://www.iit.it/en/drug-discovery-and-development/seraphic.html ). It offers computational medicinal chemists a reliable test set for both in silico protocol assessment and software development. PMID:21936510

  17. In Silico Exploration for New Antimalarials: Arylsulfonyloxy Acetimidamides as Prospective Agents.

    PubMed

    Verma, Saroj; Debnath, Utsab; Agarwal, Pooja; Srivastava, Kumkum; Prabhakar, Yenamandra S

    2015-08-24

    A strategy is described to identify new antimalarial agents to overcome the drug resistance and/or failure issues through in silico screening of multiple biological targets. As a part of this, three enzymes namely CTPS, CK, and GST were selected, from among 56 drug targets of P. falciparum, and used them in virtual screening of ZINC database entries which led to the design and synthesis of arylsulfonyloxy acetimidamides as their consensus inhibitors. From these, two compounds showed good activity against sensitive (3D7; IC50, 1.10 and 1.45 μM) and resistant (K1; IC50, 2.10 and 2.13 μM) strains of the parasite, and they were further investigated through docking and molecular dynamics simulations. The findings of this study collectively paved the way for arylsulfonyloxy acetimidamides as a new class of antimalarial agents. PMID:26237069

  18. Synthesis, crystal structure, and in vitro and in silico molecular docking of novel acyl thiourea derivatives

    NASA Astrophysics Data System (ADS)

    Haribabu, Jebiti; Subhashree, Govindarajulu Rangabashyam; Saranya, Sivaraj; Gomathi, Kannayiram; Karvembu, Ramasamy; Gayathri, Dasararaju

    2015-08-01

    In the present study, a series of six biologically active substituted acyl thiourea compounds (1-6) has been synthesized from cyclohexanecarbonyl isothiocyanate and various primary amines (2-methyl aniline, aniline, 4-methoxy aniline, 4-ethoxy aniline, benzyl amine and 2-methoxy aniline). The synthesized compounds were characterized by elemental analyses, UV-Visible, FT-IR, 1H & 13C NMR and mass spectroscopic techniques. Three dimensional molecular structure of two compounds (1 and 5) was determined by single crystal X-ray crystallography. All the synthesized compounds show good anti-oxidant and anti-haemolytic activities. In silico molecular docking studies were performed to screen against DprE1 and HSP90 enzymes targeting tuberculosis and cancer respectively.

  19. Discovery of in vitro antitubercular agents through in silico ligand-based approaches.

    PubMed

    De Vita, Daniela; Pandolfi, Fabiana; Cirilli, Roberto; Scipione, Luigi; Di Santo, Roberto; Friggeri, Laura; Mori, Mattia; Fiorucci, Diego; Maccari, Giorgio; Arul Christopher, Robert Selwyne; Zamperini, Claudio; Pau, Valentina; De Logu, Alessandro; Tortorella, Silvano; Botta, Maurizio

    2016-10-01

    The development of new anti-tubercular agents represents a constant challenge mostly due to the insurgency of resistance to the currently available drugs. In this study, a set of 60 molecules were selected by screening the Asinex and the ZINC collections and an in house library by means of in silico ligand-based approaches. Biological assays in Mycobacterium tuberculosis H37Ra ATCC 25177 strain highlighted (±)-1-(4-chlorophenyl)-2-(1H-imidazol-1-yl)ethyl-4-(3,4-dichlorophenyl)piperazine-1-carboxylate (5i) and 3-(4-chlorophenyl)-5-(2,4-dimethylpyrimidin-5-yl)-2-methylpyrazolo[1.5-a]pyrimidin-7(4H)-one (42) as the most potent compounds, having a Minimum Inhibitory Concentration (MIC) of 4 and 2 μg/mL respectively. These molecules represent a good starting point for further optimization of effective anti-TB agents. PMID:27240272

  20. State of the Art in Silico Tools for the Study of Signaling Pathways in Cancer

    PubMed Central

    Villaamil, Vanessa Medina; Gallego, Guadalupe Aparicio; Cainzos, Isabel Santamarina; Valladares-Ayerbes, Manuel; Antón Aparicio, Luis M.

    2012-01-01

    In the last several years, researchers have exhibited an intense interest in the evolutionarily conserved signaling pathways that have crucial roles during embryonic development. Interestingly, the malfunctioning of these signaling pathways leads to several human diseases, including cancer. The chemical and biophysical events that occur during cellular signaling, as well as the number of interactions within a signaling pathway, make these systems complex to study. In silico resources are tools used to aid the understanding of cellular signaling pathways. Systems approaches have provided a deeper knowledge of diverse biochemical processes, including individual metabolic pathways, signaling networks and genome-scale metabolic networks. In the future, these tools will be enormously valuable, if they continue to be developed in parallel with growing biological knowledge. In this study, an overview of the bioinformatics resources that are currently available for the analysis of biological networks is provided. PMID:22837650

  1. Physically-based in silico light sheet microscopy for visualizing fluorescent brain models

    PubMed Central

    2015-01-01

    Background We present a physically-based computational model of the light sheet fluorescence microscope (LSFM). Based on Monte Carlo ray tracing and geometric optics, our method simulates the operational aspects and image formation process of the LSFM. This simulated, in silico LSFM creates synthetic images of digital fluorescent specimens that can resemble those generated by a real LSFM, as opposed to established visualization methods producing visually-plausible images. We also propose an accurate fluorescence rendering model which takes into account the intrinsic characteristics of fluorescent dyes to simulate the light interaction with fluorescent biological specimen. Results We demonstrate first results of our visualization pipeline to a simplified brain tissue model reconstructed from the somatosensory cortex of a young rat. The modeling aspects of the LSFM units are qualitatively analysed, and the results of the fluorescence model were quantitatively validated against the fluorescence brightness equation and characteristic emission spectra of different fluorescent dyes. AMS subject classification Modelling and simulation PMID:26329404

  2. Physical characterization and in silico modeling of inulin polymer conformation during vaccine adjuvant particle formation.

    PubMed

    Barclay, Thomas G; Rajapaksha, Harinda; Thilagam, Alagu; Qian, Gujie; Ginic-Markovic, Milena; Cooper, Peter D; Gerson, Andrea; Petrovsky, Nikolai

    2016-06-01

    This study combined physical data from synchrotron SAXS, FTIR and microscopy with in-silico molecular structure predictions and mathematical modeling to examine inulin adjuvant particle formation and structure. The results show that inulin polymer chains adopt swollen random coil in solution. As precipitation occurs from solution, interactions between the glucose end group of one chain and a fructose group of an adjacent chain help drive organized assembly, initially forming inulin ribbons with helical organization of the chains orthogonal to the long-axis of the ribbon. Subsequent aggregation of the ribbons results in the layered semicrystalline particles previously shown to act as potent vaccine adjuvants. γ-Inulin adjuvant particles consist of crystalline layers 8.5nm thick comprising helically organized inulin chains orthogonal to the plane of the layer. These crystalline layers alternate with amorphous layers 2.4nm thick, to give overall particle crystallinity of 78%. PMID:27083349

  3. Arginase Flavonoid Anti-Leishmanial in Silico Inhibitors Flagged against Anti-Targets.

    PubMed

    Glisic, Sanja; Sencanski, Milan; Perovic, Vladimir; Stevanovic, Strahinja; García-Sosa, Alfonso T

    2016-01-01

    Arginase, a drug target for the treatment of leishmaniasis, is involved in the biosynthesis of polyamines. Flavonoids are interesting natural compounds found in many foods and some of them may inhibit this enzyme. The MetIDB database containing 5667 compounds was screened using an EIIP/AQVN filter and 3D QSAR to find the most promising candidate compounds. In addition, these top hits were screened in silico versus human arginase and an anti-target battery consisting of cytochromes P450 2a6, 2c9, 3a4, sulfotransferase, and the pregnane-X-receptor in order to flag their possible interactions with these proteins involved in the metabolism of substances. The resulting compounds may have promise to be further developed for the treatment of leishmaniasis. PMID:27164067

  4. Recent progresses in the exploration of machine learning methods as in-silico ADME prediction tools.

    PubMed

    Tao, L; Zhang, P; Qin, C; Chen, S Y; Zhang, C; Chen, Z; Zhu, F; Yang, S Y; Wei, Y Q; Chen, Y Z

    2015-06-23

    In-silico methods have been explored as potential tools for assessing ADME and ADME regulatory properties particularly in early drug discovery stages. Machine learning methods, with their ability in classifying diverse structures and complex mechanisms, are well suited for predicting ADME and ADME regulatory properties. Recent efforts have been directed at the broadening of application scopes and the improvement of predictive performance with particular focuses on the coverage of ADME properties, and exploration of more diversified training data, appropriate molecular features, and consensus modeling. Moreover, several online machine learning ADME prediction servers have emerged. Here we review these progresses and discuss the performances, application prospects and challenges of exploring machine learning methods as useful tools in predicting ADME and ADME regulatory properties. PMID:26037068

  5. In silico modelling of mass transfer & absorption in the human gut

    PubMed Central

    Moxon, T.E.; Gouseti, O.; Bakalis, S.

    2016-01-01

    An in silico model has been developed to investigate the digestion and absorption of starch and glucose in the small intestine. The main question we are aiming to address is the relative effect of gastric empting time and luminal viscosity on the rate of glucose absorption. The results indicate that all factors have a significant effect on the amount of glucose absorbed. For low luminal viscosities (e.g. lower than 0.1 Pas) the rate of absorption is controlled by the gastric emptying time. For viscosities higher than 0.1 Pas a 10 fold increase in viscosity can result in a 4 fold decrease of glucose absorbed. Our model, with the simplifications used to develop it, indicate that for high viscosity luminal phases, gastric emptying rate is not the controlling mechanism for nutrient availability. Developing a mechanistic model could help elucidate the rate limiting steps that control the digestion process. PMID:27143811

  6. In Silico Reconstruction of the Viral Evolutionary Lineage Yields a Potent Gene Therapy Vector.

    PubMed

    Zinn, Eric; Pacouret, Simon; Khaychuk, Vadim; Turunen, Heikki T; Carvalho, Livia S; Andres-Mateos, Eva; Shah, Samiksha; Shelke, Rajani; Maurer, Anna C; Plovie, Eva; Xiao, Ru; Vandenberghe, Luk H

    2015-08-11

    Adeno-associated virus (AAV) vectors have emerged as a gene-delivery platform with demonstrated safety and efficacy in a handful of clinical trials for monogenic disorders. However, limitations of the current generation vectors often prevent broader application of AAV gene therapy. Efforts to engineer AAV vectors have been hampered by a limited understanding of the structure-function relationship of the complex multimeric icosahedral architecture of the particle. To develop additional reagents pertinent to further our insight into AAVs, we inferred evolutionary intermediates of the viral capsid using ancestral sequence reconstruction. In-silico-derived sequences were synthesized de novo and characterized for biological properties relevant to clinical applications. This effort led to the generation of nine functional putative ancestral AAVs and the identification of Anc80, the predicted ancestor of the widely studied AAV serotypes 1, 2, 8, and 9, as a highly potent in vivo gene therapy vector for targeting liver, muscle, and retina. PMID:26235624

  7. Cloud Infrastructures for In Silico Drug Discovery: Economic and Practical Aspects

    PubMed Central

    Clematis, Andrea; Quarati, Alfonso; Cesini, Daniele; Milanesi, Luciano; Merelli, Ivan

    2013-01-01

    Cloud computing opens new perspectives for small-medium biotechnology laboratories that need to perform bioinformatics analysis in a flexible and effective way. This seems particularly true for hybrid clouds that couple the scalability offered by general-purpose public clouds with the greater control and ad hoc customizations supplied by the private ones. A hybrid cloud broker, acting as an intermediary between users and public providers, can support customers in the selection of the most suitable offers, optionally adding the provisioning of dedicated services with higher levels of quality. This paper analyses some economic and practical aspects of exploiting cloud computing in a real research scenario for the in silico drug discovery in terms of requirements, costs, and computational load based on the number of expected users. In particular, our work is aimed at supporting both the researchers and the cloud broker delivering an IaaS cloud infrastructure for biotechnology laboratories exposing different levels of nonfunctional requirements. PMID:24106693

  8. Impact of high-frequency ultrasound on nanocomposite microcapsules: in silico and in situ visualization.

    PubMed

    Korolovych, V F; Grishina, O A; Inozemtseva, O A; Selifonov, A V; Bratashov, D N; Suchkov, S G; Bulavin, L A; Glukhova, O E; Sukhorukov, G B; Gorin, D A

    2016-01-28

    The impact of high-frequency (1.2 MHz) ultrasound with a power density of 0.33 W cm(-2) on microcapsule nanocomposite shells with embedded zinc oxide nanoparticles was investigated by exploring modeling simulations and direct visualization. For the first time the sonication effect has been monitored in situ on individual microcapsules upon exposure of their aqueous suspension to ultrasound. The stress distribution on the microcapsule shell for the impact of ultrasound with high (1.2 MHz) and low (20 kHz) frequency at two fixed intensities (0.33 and 30 W cm(-2)) has been modeled. As shown in silico and experimentally the nanocomposite microcapsules were destroyed more effectively by the action of high-frequency (1.2 MHz) ultrasound in comparison to the low frequency (20 kHz) one with the same power density. PMID:26646077

  9. Molecular evolution of gas cavity in [NiFeSe] hydrogenases resurrected in silico

    PubMed Central

    Tamura, Takashi; Tsunekawa, Naoki; Nemoto, Michiko; Inagaki, Kenji; Hirano, Toshiyuki; Sato, Fumitoshi

    2016-01-01

    Oxygen tolerance of selenium-containing [NiFeSe] hydrogenases (Hases) is attributable to the high reducing power of the selenocysteine residue, which sustains the bimetallic Ni–Fe catalytic center in the large subunit. Genes encoding [NiFeSe] Hases are inherited by few sulphate-reducing δ-proteobacteria globally distributed under various anoxic conditions. Ancestral sequences of [NiFeSe] Hases were elucidated and their three-dimensional structures were recreated in silico using homology modelling and molecular dynamic simulation, which suggested that deep gas channels gradually developed in [NiFeSe] Hases under absolute anaerobic conditions, whereas the enzyme remained as a sealed edifice under environmental conditions of a higher oxygen exposure risk. The development of a gas cavity appears to be driven by non-synonymous mutations, which cause subtle conformational changes locally and distantly, even including highly conserved sequence regions. PMID:26818780

  10. Identification of SENP1 inhibitors through in silico screening and rational drug design.

    PubMed

    Zhao, Yaxue; Wang, Zhongli; Zhang, Jianchen; Zhou, Huchen

    2016-10-21

    The small ubiquitin-related modifier (SUMO)-specific proteases (SENPs) catalyze the deconjugation of SUMO from their substrate proteins. SENP1 which is the most studied isoform is closely related to many cancers such as prostate cancer and colon cancer, thus representing a potential therapeutic target for cancer treatment. In the present study, we identified eleven SENP1 inhibitors representing a variety of scaffolds through in silico screening. Based on these scaffolds, a series of new compounds were designed and synthesized in order to improve their SENP1 inhibitory potency. As a result, compounds with IC50 as low as 3.5 μM (compound 13m) were obtained and a preliminary structure-activity relationship was discussed. PMID:27344494

  11. In Silico Insight into Potential Anti-Alzheimer’s Disease Mechanisms of Icariin

    PubMed Central

    Cui, Zhijie; Sheng, Zhen; Yan, Xinmiao; Cao, Zhiwei; Tang, Kailin

    2016-01-01

    Herbal compounds that have notable therapeutic effect upon Alzheimer's disease (AD) have frequently been found, despite the recent failure of late-stage clinical drugs. Icariin, which is isolated from Epimedium brevicornum, is widely reported to exhibit significant anti-AD effects in in vitro and in vivo studies. However, the molecular mechanism remains thus far unclear. In this work, the anti-AD mechanisms of icariin were investigated at a target network level assisted by an in silico target identification program (INVDOCK). The results suggested that the anti-AD effects of icariin may be contributed by: attenuation of hyperphosphorylation of tau protein, anti-inflammation and regulation of Ca2+ homeostasis. Our results may provide assistance in understanding the molecular mechanism and further developing icariin into promising anti-AD agents. PMID:26784184

  12. In Silico Single-Molecule Manipulation of DNA with Rigid Body Dynamics

    PubMed Central

    Carrivain, Pascal; Barbi, Maria; Victor, Jean-Marc

    2014-01-01

    We develop a new powerful method to reproduce in silico single-molecule manipulation experiments. We demonstrate that flexible polymers such as DNA can be simulated using rigid body dynamics thanks to an original implementation of Langevin dynamics in an open source library called Open Dynamics Engine. We moreover implement a global thermostat which accelerates the simulation sampling by two orders of magnitude. We reproduce force-extension as well as rotation-extension curves of reference experimental studies. Finally, we extend the model to simulations where the control parameter is no longer the torsional strain but instead the torque, and predict the expected behavior for this case which is particularly challenging theoretically and experimentally. PMID:24586127

  13. Three dimensional electron microscopy and in silico tools for macromolecular structure determination

    PubMed Central

    Borkotoky, Subhomoi; Meena, Chetan Kumar; Khan, Mohammad Wahab; Murali, Ayaluru

    2013-01-01

    Recently, structural biology witnessed a major tool - electron microscopy - in solving the structures of macromolecules in addition to the conventional techniques, X-ray crystallography and nuclear magnetic resonance (NMR). Three dimensional transmission electron microscopy (3DTEM) is one of the most sophisticated techniques for structure determination of molecular machines. Known to give the 3-dimensional structures in its native form with literally no upper limit on size of the macromolecule, this tool does not need the crystallization of the protein. Combining the 3DTEM data with in silico tools, one can have better refined structure of a desired complex. In this review we are discussing about the recent advancements in three dimensional electron microscopy and tools associated with it. PMID:27092033

  14. Cloud infrastructures for in silico drug discovery: economic and practical aspects.

    PubMed

    D'Agostino, Daniele; Clematis, Andrea; Quarati, Alfonso; Cesini, Daniele; Chiappori, Federica; Milanesi, Luciano; Merelli, Ivan

    2013-01-01

    Cloud computing opens new perspectives for small-medium biotechnology laboratories that need to perform bioinformatics analysis in a flexible and effective way. This seems particularly true for hybrid clouds that couple the scalability offered by general-purpose public clouds with the greater control and ad hoc customizations supplied by the private ones. A hybrid cloud broker, acting as an intermediary between users and public providers, can support customers in the selection of the most suitable offers, optionally adding the provisioning of dedicated services with higher levels of quality. This paper analyses some economic and practical aspects of exploiting cloud computing in a real research scenario for the in silico drug discovery in terms of requirements, costs, and computational load based on the number of expected users. In particular, our work is aimed at supporting both the researchers and the cloud broker delivering an IaaS cloud infrastructure for biotechnology laboratories exposing different levels of nonfunctional requirements. PMID:24106693

  15. In silico Evolutionary Developmental Neurobiology and the Origin of Natural Language

    NASA Astrophysics Data System (ADS)

    Szathmáry, Eörs; Szathmáry, Zoltán; Ittzés, Péter; Orbaán, Geroő; Zachár, István; Huszár, Ferenc; Fedor, Anna; Varga, Máté; Számadó, Szabolcs

    It is justified to assume that part of our genetic endowment contributes to our language skills, yet it is impossible to tell at this moment exactly how genes affect the language faculty. We complement experimental biological studies by an in silico approach in that we simulate the evolution of neuronal networks under selection for language-related skills. At the heart of this project is the Evolutionary Neurogenetic Algorithm (ENGA) that is deliberately biomimetic. The design of the system was inspired by important biological phenomena such as brain ontogenesis, neuron morphologies, and indirect genetic encoding. Neuronal networks were selected and were allowed to reproduce as a function of their performance in the given task. The selected neuronal networks in all scenarios were able to solve the communication problem they had to face. The most striking feature of the model is that it works with highly indirect genetic encoding--just as brains do.

  16. Toward a complete in silico, multi-layered embryonic stem cell regulatory network

    PubMed Central

    Xu, Huilei; Schaniel, Christoph; Lemischka, Ihor R.; Ma’ayan, Avi

    2010-01-01

    Recent efforts in systematically profiling embryonic stem (ES) cells have yielded a wealth of high-throughput data. Complementarily, emerging databases and computational tools facilitate ES cell studies and further pave the way toward the in silico reconstruction of regulatory networks encompassing multiple molecular layers. Here, we briefly survey databases, algorithms, and software tools used to organize and analyze high-throughput experimental data collected to study mammalian cellular systems with a focus on ES cells. The vision of using heterogeneous data to reconstruct a complete multilayered ES cell regulatory network is discussed. This review also provides an accompanying manually extracted dataset of different types of regulatory interactions from low-throughput experimental ES cell studies available at http://amp.pharm.mssm.edu/iscmid/literature. PMID:20890967

  17. Molecular evolution of gas cavity in [NiFeSe] hydrogenases resurrected in silico.

    PubMed

    Tamura, Takashi; Tsunekawa, Naoki; Nemoto, Michiko; Inagaki, Kenji; Hirano, Toshiyuki; Sato, Fumitoshi

    2016-01-01

    Oxygen tolerance of selenium-containing [NiFeSe] hydrogenases (Hases) is attributable to the high reducing power of the selenocysteine residue, which sustains the bimetallic Ni-Fe catalytic center in the large subunit. Genes encoding [NiFeSe] Hases are inherited by few sulphate-reducing δ-proteobacteria globally distributed under various anoxic conditions. Ancestral sequences of [NiFeSe] Hases were elucidated and their three-dimensional structures were recreated in silico using homology modelling and molecular dynamic simulation, which suggested that deep gas channels gradually developed in [NiFeSe] Hases under absolute anaerobic conditions, whereas the enzyme remained as a sealed edifice under environmental conditions of a higher oxygen exposure risk. The development of a gas cavity appears to be driven by non-synonymous mutations, which cause subtle conformational changes locally and distantly, even including highly conserved sequence regions. PMID:26818780

  18. Molecular evolution of gas cavity in [NiFeSe] hydrogenases resurrected in silico

    NASA Astrophysics Data System (ADS)

    Tamura, Takashi; Tsunekawa, Naoki; Nemoto, Michiko; Inagaki, Kenji; Hirano, Toshiyuki; Sato, Fumitoshi

    2016-01-01

    Oxygen tolerance of selenium-containing [NiFeSe] hydrogenases (Hases) is attributable to the high reducing power of the selenocysteine residue, which sustains the bimetallic Ni-Fe catalytic center in the large subunit. Genes encoding [NiFeSe] Hases are inherited by few sulphate-reducing δ-proteobacteria globally distributed under various anoxic conditions. Ancestral sequences of [NiFeSe] Hases were elucidated and their three-dimensional structures were recreated in silico using homology modelling and molecular dynamic simulation, which suggested that deep gas channels gradually developed in [NiFeSe] Hases under absolute anaerobic conditions, whereas the enzyme remained as a sealed edifice under environmental conditions of a higher oxygen exposure risk. The development of a gas cavity appears to be driven by non-synonymous mutations, which cause subtle conformational changes locally and distantly, even including highly conserved sequence regions.

  19. In silico single-molecule manipulation of DNA with rigid body dynamics.

    PubMed

    Carrivain, Pascal; Barbi, Maria; Victor, Jean-Marc

    2014-02-01

    We develop a new powerful method to reproduce in silico single-molecule manipulation experiments. We demonstrate that flexible polymers such as DNA can be simulated using rigid body dynamics thanks to an original implementation of Langevin dynamics in an open source library called Open Dynamics Engine. We moreover implement a global thermostat which accelerates the simulation sampling by two orders of magnitude. We reproduce force-extension as well as rotation-extension curves of reference experimental studies. Finally, we extend the model to simulations where the control parameter is no longer the torsional strain but instead the torque, and predict the expected behavior for this case which is particularly challenging theoretically and experimentally. PMID:24586127

  20. Studies on the controllable transformation of ferrihydrite

    SciTech Connect

    Liu Hui; Ma, Miaorui; Qin, Mei; Yang, Lijuan; Wei, Yu

    2010-09-15

    Ferrihydrite was prepared by two different procedures. Ferrihydrite-1 was prepared by dropping NaOH solution into Fe(III) solution. Ferrihydrite-2 was prepared by adding Fe(III) and NaOH solutions into a certain volume of water simultaneously. Our earlier results obtained at {approx}100 {sup o}C have shown that the structure of ferrihydrite-2 favors its solid state transformation mechanism. Further research reveals that the structure of ferrihydrite-2 favors its dissolution re-crystallization mechanism at a temperature of {<=}60 {sup o}C. Based on the transformation mechanism of ferrihydrite at different temperatures, the controllable transformation from ferrihydrite to various iron (hydr)oxides such as lepidocrocite, goethite, hematite and magnetite can be achieved by adjusting the pH, transformation temperature, transformation time, the amount of Fe(II) as well as the preparation procedures of ferrihydrite. The results in the present paper give a nice example that the transformation of a precursor can be controlled with the help of mechanism. - Graphical abstract: The transformations from ferrihydrite to lepidocrocite, goethite, hematite or magnetite can be controlled with the help of mechanism.

  1. Evaluation of selectivity in homologous multimodal chromatographic systems using in silico designed antibody fragment libraries.

    PubMed

    Karkov, Hanne Sophie; Woo, James; Krogh, Berit Olsen; Ahmadian, Haleh; Cramer, Steven M

    2015-12-24

    This study describes the in silico design, surface property analyses, production and chromatographic evaluations of a diverse set of antibody Fab fragment variants. Based on previous findings, we hypothesized that the complementarity-determining regions (CDRs) constitute important binding sites for multimodal chromatographic ligands. Given that antibodies are highly diversified molecules and in particular the CDRs, we set out to examine the generality of this result. For this purpose, four different Fab fragments with different CDRs and/or framework regions of the variable domains were identified and related variants were designed in silico. The four Fab variant libraries were subsequently generated by site-directed mutagenesis and produced by recombinant expression and affinity purification to enable examination of their chromatographic retention behavior. The effects of geometric re-arrangement of the functional moieties on the multimodal resin ligands were also investigated with respect to Fab variant retention profiles by comparing two commercially available multimodal cation-exchange ligands, Capto MMC and Nuvia cPrime, and two novel multimodal ligand prototypes. Interestingly, the chromatographic data demonstrated distinct selectivity trends between the four Fab variant libraries. For three of the Fab libraries, the CDR regions appeared as major binding sites for all multimodal ligands. In contrast, the fourth Fab library displayed a distinctly different chromatographic behavior, where Nuvia cPrime and related multimodal ligand prototypes provided markedly improved selectivity over Capto MMC. Clearly, the results illustrate that the discriminating power of multimodal ligands differs between different Fab fragments. The results are promising indications that multimodal chromatography using the appropriate multimodal ligands can be employed in downstream bioprocessing for challenging selective separation of product related variants. PMID:26654254

  2. Silico-tuberculosis and associated risk factors in central province of Iran

    PubMed Central

    Farazi, Aliasghar; Jabbariasl, Mansooreh

    2015-01-01

    Introduction Co-existence of silicosis and tuberculosis is known as silico-tuberculosis. This article review the frequency of silicosis and tuberculosis in workers who exposed to silica and evaluate influencing factors that may increase the risk of silico-tuberculosis. Methods An analytical cross-sectional study was performed in silica exposed workers in central province of Iran during 2011-2012. Sampling method was un-randomized and considering all workers who at least 6 months exposed to silica. The study was done via questionnaire, clinical examination, spirometry, chest x-ray and tuberculosis investigations. Results A total of 3121 workers were included in the study, the mean age of participants was 43.1±12.4 years, and mean employment duration 14.9±6.8 years. Prevalence of TB in silica-exposed workers without silicosis was 172 cases per 100 000 people and prevalence in silicosis cases was 917 cases per 100 000 people. Incidence of TB in silica-exposed workers without silicosis was 69 cases per 100 000 people and incidence in silicosis cases was 459 cases per 100 000 people. The frequency of LTBI/TB was higher in age over thirty years old (P = 0.02), in workers with employment duration over 10 years (P = 0.004), in workers with exposure duration over 5 years (P = 0.03) and smokers with over 5 pack-years (P = 0.01). Conclusion Exposure to silica causes a renewed multiplication of bacilli in the healing TB lesions. Prevalence of pulmonary tuberculosis in Silicosis is more common when compared to prevalence in general population, hence all should use prophylactic measures Intensification of work place. PMID:26175823

  3. In silico identification of IgE-binding epitopes of osmotin protein.

    PubMed

    Sharma, Prerna; Gaur, Shailendra Nath; Arora, Naveen

    2013-01-01

    The identification of B-cell epitopes is an important step to study the antigen- antibody interactions for diagnosis and therapy. The present study aimed to identify B- cell epitopes of osmotin using bioinformatic tools and further modify these regions to study the allergenic property. B-cell epitopes were predicted based on amino acid physicochemical properties. Three single point mutations M1, M2, and M3 and a multiple point mutant (M123) were selected to disrupt the IgE binding. These mutants were cloned, expressed and proteins purified to homogeneity. The IgE binding of the purified proteins was evaluated by ELISA and ELISA inhibition with patients' sera. Three regions of osmotin M1 (57-70 aa), M2 (72-85 aa) and M3 (147-165 aa) were identified as potential antibody recognition sites using in silico tools. The sequence similarity search of the predicted epitopes of osmotin using Structural Database of Allergenic proteins (SDAP) showed similarity with known allergens from tomato, kiwifruit, bell pepper, apple, mountain cedar and cypress. Mutants M1, M2 and M3 showed up to 72%, 60% and 76% reduction, respectively in IgE binding whereas M123 showed up to 90% reduction with patients' sera. The immunoblot of M123 mutant showed 40% reduction in spot density as compared to osmotin. All mutants showed decreased inhibition potency with M123 exhibiting lowest potency of 32% with osmotin positive pooled patients' sera. The three B- cell epitopes of osmotin predicted by in silico method correlated with the experimental approach. The mutant M123 showed a reduction of 90% in IgE binding. The present method may be employed for prediction of B- cell epitopes of allergenic proteins. PMID:23349964

  4. Generation of random numbers on graphics processors: forced indentation in silico of the bacteriophage HK97.

    PubMed

    Zhmurov, A; Rybnikov, K; Kholodov, Y; Barsegov, V

    2011-05-12

    The use of graphics processing units (GPUs) in simulation applications offers a significant speed gain as compared to computations on central processing units (CPUs). Many simulation methods require a large number of independent random variables generated at each step. We present two approaches for implementation of random number generators (RNGs) on a GPU. In the one-RNG-per-thread approach, one RNG produces a stream of random numbers in each thread of execution, whereas the one-RNG-for-all-threads method builds on the ability of different threads to communicate, thus, sharing random seeds across an entire GPU device. We used these approaches to implement Ran2, Hybrid Taus, and Lagged Fibonacci algorithms on a GPU. We profiled the performance of these generators in terms of the computational time, memory usage, and the speedup factor (CPU time/GPU time). These generators have been incorporated into the program for Langevin simulations of biomolecules fully implemented on the GPU. The ∼250-fold computational speedup on the GPU allowed us to carry out single-molecule dynamic force measurements in silico to explore the mechanical properties of the bacteriophage HK97 in the experimental subsecond time scale. We found that the nanomechanical response of HK97 depends on the conditions of force application, including the rate of change and geometry of the mechanical perturbation. Hence, using the GPU-based implementation of RNGs, presented here, in conjunction with Langevin simulations, makes it possible to directly compare the results of dynamic force measurements in vitro and in silico. PMID:21194190

  5. Initial evaluation of Sandia National Laboratory-prepared crystalline silico-titanates for cesium recovery

    SciTech Connect

    Bray, L.A.; Carson, K.J.; Elovich, R.J.

    1993-10-01

    Pacific Northwest Laboratory initiated a study of a new class of inorganic ion exchange materials that selectively extracts cesium (Cs), strontium (Sr), and plutonium (Pu) from alkaline radioactive waste solutions. These materials, identified as crystalline silico-titanates (CST), were developed by scientists at the Sandia National Laboratory (SNL) and Texas A&M. This report summarizes preliminary results for the measurement of batch distribution coefficient (K{sub d}) values for the powdered CST materials compared to previously tested ion exchange materials: IONSIV IE-96 (a zeolite produced by UOP), CS-100 (an organic resin produced by Rohm and Haas), and BIB-DJ (a new resorcinol-formaldehyde organic resin produced by Boulder Scientific). Excellent results were obtained for CST inorganic exchangers that could be significant in the development of processes for the near-term pretreatment of Hanford alkaline wastes. The following observations and conclusions resulted from this study: (1) Several CST samples prepared at SNL had a higher capacity to remove Cs from solution as compared to BIB-DJ, IE-96, and CS-100. (2) Cesium distribution results showed that CST samples TAM-40, -42, -43, -70, and -74 had {lambda} values of {approximately}2,200 ({lambda} = Cs K{sub d} {times} {rho}{sub b}; where {lambda} represents the number of exchanger bed volumes of feed that can be loaded on an ion exchange column) at a pH value >14. (3) Cesium distribution values for CST exchangers doubled as the aqueous temperature decreased from 40{degrees} to 10{degrees}C. (4) Crystalline silico-titanates have the capacity to remove Cs as well as Sr and Pu from alkaline wastes unless organic complexants are present. Experimental results indicated that complexed Sr was not removed, and Pu is not expected to be removed.

  6. In silico prioritization based on coexpression can aid epileptic encephalopathy gene discovery

    PubMed Central

    Oliver, Karen L.; Lukic, Vesna; Freytag, Saskia; Scheffer, Ingrid E.; Berkovic, Samuel F.

    2016-01-01

    Objective: To evaluate the performance of an in silico prioritization approach that was applied to 179 epileptic encephalopathy candidate genes in 2013 and to expand the application of this approach to the whole genome based on expression data from the Allen Human Brain Atlas. Methods: PubMed searches determined which of the 179 epileptic encephalopathy candidate genes had been validated. For validated genes, it was noted whether they were 1 of the 19 of 179 candidates prioritized in 2013. The in silico prioritization approach was applied genome-wide; all genes were ranked according to their coexpression strength with a reference set (i.e., 51 established epileptic encephalopathy genes) in both adult and developing human brain expression data sets. Candidate genes ranked in the top 10% for both data sets were cross-referenced with genes previously implicated in the epileptic encephalopathies due to a de novo variant. Results: Five of 6 validated epileptic encephalopathy candidate genes were among the 19 prioritized in 2013 (odds ratio = 54, 95% confidence interval [7,∞], p = 4.5 × 10−5, Fisher exact test); one gene was false negative. A total of 297 genes ranked in the top 10% for both the adult and developing brain data sets based on coexpression with the reference set. Of these, 9 had been previously implicated in the epileptic encephalopathies (FBXO41, PLXNA1, ACOT4, PAK6, GABBR2, YWHAG, NBEA, KNDC1, and SELRC1). Conclusions: We conclude that brain gene coexpression data can be used to assist epileptic encephalopathy gene discovery and propose 9 genes as strong epileptic encephalopathy candidates worthy of further investigation. PMID:27066588

  7. Inducibility of human atrial fibrillation in an in silico model reflecting local acetylcholine distribution and concentration.

    PubMed

    Hwang, Minki; Lee, Hyun-Seung; Pak, Hui-Nam; Shim, Eun Bo

    2016-01-01

    Vagal nerve activity has been known to play a crucial role in the induction and maintenance of atrial fibrillation (AF). However, it is unclear how the distribution and concentration of local acetylcholine (ACh) promotes AF. In this study, we investigated the effect of the spatial distribution and concentration of ACh on fibrillation patterns in an in silico human atrial model. A human atrial action potential model with an ACh-dependent K(+) current (IKAch) was used to examine the effect of vagal activation. A simulation of cardiac wave dynamics was performed in a realistic 3D model of the atrium. A model of the ganglionated plexus (GP) and nerve was developed based on the "octopus hypothesis". The pattern of cardiac wave dynamics was examined by applying vagal activation to the GP areas or randomly. AF inducibility in the octopus hypothesis-based GP and nerve model was tested. The effect of the ACh concentration level was also examined. In the single cell simulation, an increase in the ACh concentration shortened APD90 and increased the maximal slope of the restitution curve. In the 3D simulation, a random distribution of vagal activation promoted wavebreaks while ACh secretion limited to the GP areas did not induce a noticeable change in wave dynamics. The octopus hypothesis-based model of the GP and nerve exhibited AF inducibility at higher ACh concentrations. In conclusion, a 3D in silico model of the GP and parasympathetic nerve based on the octopus model exhibited higher AF inducibility with higher ACh concentrations. PMID:26807030

  8. A practical application of two in silico systems for identification of potentially mutagenic impurities.

    PubMed

    Greene, Nigel; Dobo, Krista L; Kenyon, Michelle O; Cheung, Jennifer; Munzner, Jennifer; Sobol, Zhanna; Sluggett, Gregory; Zelesky, Todd; Sutter, Andreas; Wichard, Joerg

    2015-07-01

    The International Conference on Harmonization (ICH) M7 guidance for the assessment and control of DNA reactive impurities in pharmaceutical products includes the use of in silico prediction systems as part of the hazard identification and risk assessment strategy. This is the first internationally agreed guidance document to include the use of these types of approaches. The guideline requires the use of two complementary approaches, an expert rule-based method and a statistical algorithm. In addition, the guidance states that the output from these computer-based assessments can be reviewed using expert knowledge to provide additional support or resolve conflicting predictions. This approach is designed to maximize the sensitivity for correctly identifying DNA reactive compounds while providing a framework to reduce the number of compounds that need to be synthesized, purified and subsequently tested in an Ames assay. Using a data set of 801 chemicals and pharmaceutical intermediates, we have examined the relative predictive performances of some popular commercial in silico systems that are in common use across the pharmaceutical industry. The overall accuracy of each of these systems was fairly comparable ranging from 68% to 73%; however, the sensitivity of each system (i.e. how many Ames positive compounds are correctly identified) varied much more dramatically from 48% to 68%. We have explored how these systems can be combined under the ICH M7 guidance to enhance the detection of DNA reactive molecules. Finally, using four smaller sets of molecules, we have explored the value of expert knowledge in the review process, especially in cases where the two systems disagreed on their predictions, and the need for care when evaluating the predictions for large data sets. PMID:25980641

  9. In silico assessment of drug safety in human heart applied to late sodium current blockers

    PubMed Central

    Trenor, Beatriz; Gomis-Tena, Julio; Cardona, Karen; Romero, Lucia; Rajamani, Sridharan; Belardinelli, Luiz; Giles, Wayne R; Saiz, Javier

    2013-01-01

    Drug-induced action potential (AP) prolongation leading to Torsade de Pointes is a major concern for the development of anti-arrhythmic drugs. Nevertheless the development of improved anti-arrhythmic agents, some of which may block different channels, remains an important opportunity. Partial block of the late sodium current (INaL) has emerged as a novel anti-arrhythmic mechanism. It can be effective in the settings of free radical challenge or hypoxia. In addition, this approach can attenuate pro-arrhythmic effects of blocking the rapid delayed rectifying K+ current (IKr). The main goal of our computational work was to develop an in-silico tool for preclinical anti-arrhythmic drug safety assessment, by illustrating the impact of IKr/INaL ratio of steady-state block of drug candidates on “torsadogenic” biomarkers. The O’Hara et al. AP model for human ventricular myocytes was used. Biomarkers for arrhythmic risk, i.e., AP duration, triangulation, reverse rate-dependence, transmural dispersion of repolarization and electrocardiogram QT intervals, were calculated using single myocyte and one-dimensional strand simulations. Predetermined amounts of block of INaL and IKr were evaluated. “Safety plots” were developed to illustrate the value of the specific biomarker for selected combinations of IC50s for IKr and INaL of potential drugs. The reference biomarkers at baseline changed depending on the “drug” specificity for these two ion channel targets. Ranolazine and GS967 (a novel potent inhibitor of INaL) yielded a biomarker data set that is considered safe by standard regulatory criteria. This novel in-silico approach is useful for evaluating pro-arrhythmic potential of drugs and drug candidates in the human ventricle. PMID:23696033

  10. Studies on interaction of norbixin with DNA: multispectroscopic and in silico analysis.

    PubMed

    Anantharaman, Amrita; Priya, Rajendra Rao; Hemachandran, Hridya; Sivaramakrishna, Akella; Babu, Subramanian; Siva, Ramamoorthy

    2015-06-01

    The interaction of food colorant norbixin with calf thymus DNA (CTDNA) was investigated through UV-Visible spectroscopy, Fourier Transform Infrared (FTIR), Circular Dichroism (CD), Nuclear Magnetic Resonance (NMR), DNA melting studies, electrophoretic analysis, histological staining technique and molecular docking studies. The results indicated that norbixin interacted with CTDNA by partial intercalation mode. The binding constant (K) of norbixin with CTDNA was calculated to be 5.08×10(5) Mol(-1) L. FTIR and CD studies were coupled with (1)H NMR spectra revealed that norbixin intercalates partially and binds to the groove's, phosphate group, deoxyribose sugar of DNA and also induces conformational transition of B-form to A-form DNA. Agarose gel electrophoretic and histological staining technique results further prove that, norbixin specifically binds to the DNA in the cell. Moreover, molecular docking studies on the specific binding of norbixin with CTDNA have exhibited lowest conformation energy score of -3.2. Therefore, this food colorant has the ability to interact with DNA and it could emerge as a promising class of natural DNA targeted therapeutic. PMID:25754392

  11. Studies on interaction of norbixin with DNA: Multispectroscopic and in silico analysis

    NASA Astrophysics Data System (ADS)

    Anantharaman, Amrita; Priya, Rajendra Rao; Hemachandran, Hridya; Sivaramakrishna, Akella; Babu, Subramanian; Siva, Ramamoorthy

    2015-06-01

    The interaction of food colorant norbixin with calf thymus DNA (CTDNA) was investigated through UV-Visible spectroscopy, Fourier Transform Infrared (FTIR), Circular Dichroism (CD), Nuclear Magnetic Resonance (NMR), DNA melting studies, electrophoretic analysis, histological staining technique and molecular docking studies. The results indicated that norbixin interacted with CTDNA by partial intercalation mode. The binding constant (K) of norbixin with CTDNA was calculated to be 5.08 × 105 Mol-1 L. FTIR and CD studies were coupled with 1H NMR spectra revealed that norbixin intercalates partially and binds to the groove's, phosphate group, deoxyribose sugar of DNA and also induces conformational transition of B-form to A-form DNA. Agarose gel electrophoretic and histological staining technique results further prove that, norbixin specifically binds to the DNA in the cell. Moreover, molecular docking studies on the specific binding of norbixin with CTDNA have exhibited lowest conformation energy score of -3.2. Therefore, this food colorant has the ability to interact with DNA and it could emerge as a promising class of natural DNA targeted therapeutic.

  12. InSilico DB genomic datasets hub: an efficient starting point for analyzing genome-wide studies in GenePattern, Integrative Genomics Viewer, and R/Bioconductor

    PubMed Central

    2012-01-01

    Genomics datasets are increasingly useful for gaining biomedical insights, with adoption in the clinic underway. However, multiple hurdles related to data management stand in the way of their efficient large-scale utilization. The solution proposed is a web-based data storage hub. Having clear focus, flexibility and adaptability, InSilico DB seamlessly connects genomics dataset repositories to state-of-the-art and free GUI and command-line data analysis tools. The InSilico DB platform is a powerful collaborative environment, with advanced capabilities for biocuration, dataset sharing, and dataset subsetting and combination. InSilico DB is available from https://insilicodb.org. PMID:23158523

  13. Cultural Adaptation of Headmasters' Transformational Leadership Scale and a Study on Teachers' Perceptions

    ERIC Educational Resources Information Center

    Balyer, Aydin; Özcan, Kenan

    2012-01-01

    Problem Statement: Transformational leadership increases organization members' commitment and engagement in meeting organizational goals and it enhances skills and capacities. Many studies reveal that transformational leadership behaviors, such as idealized influence, inspirational motivation, individualized consideration, innovative climate, and…

  14. The duality principle and inversion of Laplace-Stielties transforms

    NASA Astrophysics Data System (ADS)

    Pavelyev, A. G.

    2016-04-01

    The fundamental relation between the Laplace transform, the Stielties transform, and the generalized integral equation of refraction is revealed, and a duality principle is formulated for the solution of inverse problems of radio physics. New formulas of the Laplace-transform inversion satisfying the duality principle are obtained. There is no necessity of contour integration in a complex plane for the relations found, which considerably simplifies the reconstruction of originals and makes it possible to control systematic errors in the experimental data.

  15. In silico Analysis for Predicting Fatty Acids of Black Cumin Oil as Inhibitors of P-Glycoprotein

    PubMed Central

    Ali, Babar; Jamal, Qazi Mohd. Sajid; Mir, Showkat R.; Shams, Saiba; Al-Wabel, Naser A.; Kamal, Mohammad A.

    2015-01-01

    Background: Black cumin oil is obtained from the seeds of Nigella sativa L. which belongs to family Ranunculaceae. The seed oil has been reported to possess antitumor, antioxidant, antibacterial, anti-inflammatory, hypoglycemic, central nervous system depressant, antioxidant, and immunostimulatory activities. These bioactivities have been attributed to the fixed oil, volatile oil, or their components. Seed oil consisted of 15 saturated fatty acids (17%) and 17 unsaturated fatty acids (82.9%). Long chain fatty acids and medium chain fatty acids have been reported to increase oral bioavailability of peptides, antibiotics, and other important therapeutic agents. In earlier studies, permeation enhancement and bioenhancement of drugs has been done with black cumin oil. Objective: In order to recognize the mechanism of binding of fatty acids to P-glycoprotein (P-gp), linoleic acid, oleic acid, margaric acid, cis-11, 14-eicosadienoic acid, and stearic acid were selected for in silico studies, which were carried out using AutoDock 4.2, based on the Lamarckian genetic algorithm principle. Materials and Methods: Template search with BLAST and HHblits has been performed against the SWISS-MODEL template library. The target sequence was searched with BLAST against the primary amino acid sequence of P-gp from Rattus norvegicus. Results: The amount of energy needed by linoleic acid, oleic acid, eicosadienoic acid, margaric acid, and stearic acid to bind with P-gp were found to be − 10.60, −10.48, −9.95, −11.92, and − 10.37 kcal/mol, respectively. The obtained data support that all the selected fatty acids have contributed to inhibit P-gp activity thereby enhances the bioavailability of drugs. Conclusion: This study plays a significant role in finding hot spots in P-gp and may offer the further scope of designing potent and specific inhibitors of P-gp. SUMMARY Generation of 3D structure of fatty acid compounds from Black cumin oil and 3D homology modeling of Rat P

  16. Fullerenol C60(OH)16 prevents amyloid fibrillization of Aβ40-in vitro and in silico approach.

    PubMed

    Bednarikova, Zuzana; Huy, Pham Dinh Quoc; Mocanu, Maria-Magdalena; Fedunova, Diana; Li, Mai Suan; Gazova, Zuzana

    2016-07-28

    The generation of Aβ amyloid aggregates in the form of senile plaques in the brain is one of the pathological hallmarks of Alzheimer's disease (AD). There is no cure for AD and one of the recent treatment strategies is focused on the inhibition of amyloid fibrillization of Aβ peptide. Fullerene C60 has been proposed as a candidate for destroying Aβ aggregates but it is not soluble in water and its toxicity to cells remains largely ambiguous. To overcome these drawbacks, we synthesized and studied the effect of water-soluble fullerenol C60(OH)16 (fullerene C60 carrying 16 hydroxyl groups) on the amyloid fibrillization of Aβ40 peptide in vitro. Using a Thioflavin T fluorescent assay and atomic force microscopy it was found that C60(OH)16 effectively reduces the formation of amyloid fibrils. The IC50 value is in the low range (μg ml(-1)) suggesting that fullerenol interferes with Aβ40 aggregation at stoichiometric concentrations. The in silico calculations supported the experimental data. It was revealed that fullerenol tightly binds to monomer Aβ40 and polar, negatively charged amino acids play a key role. Electrostatic interactions dominantly contribute to the binding propensity via interaction of the oxygen atoms from the COO(-) groups of side chains of polar, negatively charged amino acids with the OH groups of fullerenol. This stabilizes contact with either the D23 or K28 of the salt bridge. Due to the lack of a well-defined binding pocket fullerenol is also inclined to locate near the central hydrophobic region of Aβ40 and can bind to the hydrophobic C-terminal of the peptide. Upon fullerenol binding the salt bridge becomes flexible, inhibiting Aβ aggregation. In order to assess the toxicity of fullerenol, we found that exposure of neuroblastoma SH-SY5Y cells to fullerenol caused no significant changes in viability after 24 h of treatment. These results suggest that fullerenol C60(OH)16 represents a promising candidate as a therapeutic for Alzheimer

  17. In silico evidence for the species-specific conservation of mosquito retroposons: implications as a molecular biomarker

    PubMed Central

    Byarugaba, Wilson; Kajumbula, Henry; Wayengera, Misaki

    2009-01-01

    Background Mosquitoes are the transmissive vectors for several infectious pathogens that affect man. However, the control of mosquitoes through insecticide and pesticide spraying has proved difficult in the past. We hypothesized that, by virtue of their reported vertical inheritance among mosquitoes, group II introns – a class of small coding ribonucleic acids (scRNAs) – may form a potential species-specific biomarker. Structurally, introns are a six-moiety complex. Depending on the function of the protein encoded within the IV moiety, the highly mobile class of group II introns or retroposons is sub-divided into two: Restriction Endonuclease (REase)-like and Apurinic aPyramydinic Endonuclease (APE)-like. REase-like retroposons are thought to be the ancestors of APE retroposons. Our aim in this study was to find evidence for the highly species-specific conservation of the APE subclass of mosquito retroposons. Methods and Results In silico targeted sequence alignments were conducted across a 1,779-organism genome database (1,518 bacterial, 59 archeal, 201 eukaryotic, and the human), using three mosquito retroposon sequence tags (RST) as BLASTN queries [AJ970181 and AJ90201 of Culex pipien origin and AJ970301 of Anoplese sinensis origin]. At a calibration of E = 10, A & D = 100, default filtration and a homology cut-off of >95% identity, no hits were found on any of the 1,518 bacterial genomes. Eleven (100%) and 15 (100%) hits obtained on the 201-eukaryote genome database were homologs (>95% score) of C.pipien quinquefasciatus JHB retroposons, but none of An. sinensis. Twenty and 221 low score (30–43% identity) spurious hits were found at flanking ends of genes and contigs in the human genome with the C.pipien and An. sinensis RSTs respectively. Functional and positional inference revealed these to be possible relatives of human genomic spliceosomes. We advance two models for the application of mosquito RST: as precursors for developing molecular biomarkers for

  18. Transformer design tradeoffs

    NASA Technical Reports Server (NTRS)

    Mclyman, W. T.

    1976-01-01

    Material was presented to assist transformer designers in the transition from long-used English units to the less familiar metric equivalents. A coordination between the area product numbers ap (product of window and core cross-section areas) and current density J was developed for a given regulation and temperature rise. Straight-line relationships for Ap and Volume, Ap and surface area At and, Ap and weight were developed. These relationships can now be used as new tools to simplify and standardize the process of transformer design. They also made it possible to design transformers of small bulk and volume or to optimize efficiency.

  19. Optical sine transformation.

    PubMed

    Yang, G; Zhang, J; Gong, J; Chen, J; Ho, Y

    1987-10-15

    The phase mask distribution of optical sine transformation (OST) has been calculated according to the optical general transformation theory. To avoid the diffraction loss of the phase mask, the optical waveguide method is used. Computation shows that the optical sine transformation is possible with only one phase mask, i.e., one-half of a cylindrical lens in the 1-D case and one-quarter of a spherical lens in the 2-D case. Experimental results agree with the theoretical prediction. Image compression by OST is also given. PMID:20523380

  20. High-Performance Work Systems: American Models of Workplace Transformation.

    ERIC Educational Resources Information Center

    Appelbaum, Eileen; Batt, Rosemary

    Rising competition in world and domestic markets for the past 2 decades has necessitated that U.S. companies undergo significant transformations to improve their performance with respect to a wide array of efficiency and quality indicators. Research on the transformations recently undertaken by some U.S. companies to boost performance revealed two…

  1. Advances in the Natural transform

    NASA Astrophysics Data System (ADS)

    Belgacem, F. B. M.; Silambarasan, R.

    2012-11-01

    The literature review of the Natural transform and the existing definitions and connections to the Laplace and Sumudu transforms are discussed in this communication. Along with the complex inverse Natural transform and Heaviside's expansion formula, the relation of Bessel's function to Natural transform (and hence Laplace and Sumudu transforms) are defined.

  2. A discrete fractional random transform

    NASA Astrophysics Data System (ADS)

    Liu, Zhengjun; Zhao, Haifa; Liu, Shutian

    2005-11-01

    We propose a discrete fractional random transform based on a generalization of the discrete fractional Fourier transform with an intrinsic randomness. Such discrete fractional random transform inheres excellent mathematical properties of the fractional Fourier transform along with some fantastic features of its own. As a primary application, the discrete fractional random transform has been used for image encryption and decryption.

  3. A Classical Science Transformed.

    ERIC Educational Resources Information Center

    Kovalevsky, Jean

    1979-01-01

    Describes how satellites and other tools of space technology have transformed classical geodesy into the science of space geodynamics. The establishment and the activities of the French Center for Geodynamic and Astronomical Research Studies (CERGA) are also included. (HM)

  4. Transformer design tradeoffs

    NASA Technical Reports Server (NTRS)

    Mclyman, W. T.

    1977-01-01

    In space, power system transformer components are frequently the heaviest and bulkiest items in the power conversion circuit. They also have a significant effect upon the overall performance and efficiency of the system. Accordingly, the design of such transformers has an important effect on overall system weight, power-inversion efficiency, and cost. Relationships were between the parameters used by transformer designers that can be used as new tools to standardize and simplify transformer design. They can be used to optimize the design either for small size and weight or efficiency. The metric system of units, rather than the familiar English units, is used; however, material is presented to assist the reader in the transition from one system to the other.

  5. Imaging Fourier transform spectrometer

    SciTech Connect

    Bennett, C.L.

    1993-09-13

    This invention is comprised of an imaging Fourier transform spectrometer having a Fourier transform infrared spectrometer providing a series of images to a focal plane array camera. The focal plane array camera is clocked to a multiple of zero crossing occurrences as caused by a moving mirror of the Fourier transform infrared spectrometer and as detected by a laser detector such that the frame capture rate of the focal plane array camera corresponds to a multiple of the zero crossing rate of the Fourier transform infrared spectrometer. The images are transmitted to a computer for processing such that representations of the images as viewed in the light of an arbitrary spectral ``fingerprint`` pattern can be displayed on a monitor or otherwise stored and manipulated by the computer.

  6. Fourier Transform Mass Spectrometry

    PubMed Central

    Scigelova, Michaela; Hornshaw, Martin; Giannakopulos, Anastassios; Makarov, Alexander

    2011-01-01

    This article provides an introduction to Fourier transform-based mass spectrometry. The key performance characteristics of Fourier transform-based mass spectrometry, mass accuracy and resolution, are presented in the view of how they impact the interpretation of measurements in proteomic applications. The theory and principles of operation of two types of mass analyzer, Fourier transform ion cyclotron resonance and Orbitrap, are described. Major benefits as well as limitations of Fourier transform-based mass spectrometry technology are discussed in the context of practical sample analysis, and illustrated with examples included as figures in this text and in the accompanying slide set. Comparisons highlighting the performance differences between the two mass analyzers are made where deemed useful in assisting the user with choosing the most appropriate technology for an application. Recent developments of these high-performing mass spectrometers are mentioned to provide a future outlook. PMID:21742802

  7. Fractals and Transformations.

    ERIC Educational Resources Information Center

    Bannon, Thomas J.

    1991-01-01

    Discussed are several different transformations based on the generation of fractals including self-similar designs, the chaos game, the koch curve, and the Sierpinski Triangle. Three computer programs which illustrate these concepts are provided. (CW)

  8. Proof in Transformation Geometry

    ERIC Educational Resources Information Center

    Bell, A. W.

    1971-01-01

    The first of three articles showing how inductively-obtained results in transformation geometry may be organized into a deductive system. This article discusses two approaches to enlargement (dilatation), one using coordinates and the other using synthetic methods. (MM)

  9. Nontensorial Transformation Optics

    NASA Astrophysics Data System (ADS)

    García-Meca, C.; Barceló, C.

    2016-06-01

    We present an alternative version of transformation optics that allows us to mold the flow of light without rotating or scaling the electromagnetic fields. The resulting media experience unusual force densities, are nonreciprocal, and exhibit loss or gain. Because of these singular features, a variety of effects and devices unreachable by standard transformation optics can be achieved, including reflectionless light compression, optical modes with arbitrary in-plane polarization, and special isolators.

  10. Series Transmission Line Transformer

    DOEpatents

    Buckles, Robert A.; Booth, Rex; Yen, Boris T.

    2004-06-29

    A series transmission line transformer is set forth which includes two or more of impedance matched sets of at least two transmissions lines such as shielded cables, connected in parallel at one end ans series at the other in a cascading fashion. The cables are wound about a magnetic core. The series transmission line transformer (STLT) which can provide for higher impedance ratios and bandwidths, which is scalable, and which is of simpler design and construction.

  11. In silico design, synthesis and evaluation of 3'-O-benzylated analogs of salacinol, a potent α-glucosidase inhibitor isolated from an Ayurvedic traditional medicine "Salacia".

    PubMed

    Tanabe, Genzoh; Nakamura, Shinya; Tsutsui, Nozomi; Balakishan, Gorre; Xie, Weijia; Tsuchiya, Satoshi; Akaki, Junji; Morikawa, Toshio; Ninomiya, Kiyofumi; Nakanishi, Isao; Yoshikawa, Masayuki; Muraoka, Osamu

    2012-09-01

    With the aid of an in silico method, α-glucosidase inhibitors with far more potent activities than salacinol (1), a potent natural α-glucosidase inhibitor isolated from an Ayurvedic traditional medicine Salacia reticulata, have been developed. PMID:22820468

  12. 25. VIEW, LOOKING SOUTHWEST INSIDE TRANSFORMER ROOM, SHOWING TRANSFORMERS AND ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    25. VIEW, LOOKING SOUTHWEST INSIDE TRANSFORMER ROOM, SHOWING TRANSFORMERS AND KNIFE SWITCHES - Sacramento River Bridge, Spanning Sacramento River at California State Highway 275, Sacramento, Sacramento County, CA

  13. Structure-based in silico identification of ubiquitin-binding domains provides insights into the ALIX-V:ubiquitin complex and retrovirus budding

    PubMed Central

    Keren-Kaplan, Tal; Attali, Ilan; Estrin, Michael; Kuo, Lillian S; Farkash, Efrat; Jerabek-Willemsen, Moran; Blutraich, Noa; Artzi, Shay; Peri, Aviyah; Freed, Eric O; Wolfson, Haim J; Prag, Gali

    2013-01-01

    The ubiquitylation signal promotes trafficking of endogenous and retroviral transmembrane proteins. The signal is decoded by a large set of ubiquitin (Ub) receptors that tether Ub-binding domains (UBDs) to the trafficking machinery. We developed a structure-based procedure to scan the protein data bank for hidden UBDs. The screen retrieved many of the known UBDs. Intriguingly, new potential UBDs were identified, including the ALIX-V domain. Pull-down, cross-linking and E3-independent ubiquitylation assays biochemically corroborated the in silico findings. Guided by the output model, we designed mutations at the postulated ALIX-V:Ub interface. Biophysical affinity measurements using microscale-thermophoresis of wild-type and mutant proteins revealed some of the interacting residues of the complex. ALIX-V binds mono-Ub with a Kd of 119 μM. We show that ALIX-V oligomerizes with a Hill coefficient of 5.4 and IC50 of 27.6 μM and that mono-Ub induces ALIX-V oligomerization. Moreover, we show that ALIX-V preferentially binds K63 di-Ub compared with mono-Ub and K48 di-Ub. Finally, an in vivo functionality assay demonstrates the significance of ALIX-V:Ub interaction in equine infectious anaemia virus budding. These results not only validate the new procedure, but also demonstrate that ALIX-V directly interacts with Ub in vivo and that this interaction can influence retroviral budding. PMID:23361315

  14. Identification of possible siRNA molecules for TDP43 mutants causing amyotrophic lateral sclerosis: In silico design and molecular dynamics study.

    PubMed

    Bhandare, Vishwambhar Vishnu; Ramaswamy, Amutha

    2016-04-01

    The DNA binding protein, TDP43 is a major protein involved in amyotrophic lateral sclerosis and other neurological disorders such as frontotemporal dementia, Alzheimer disease, etc. In the present study, we have designed possible siRNAs for the glycine rich region of tardbp mutants causing ALS disorder based on a systematic theoretical approach including (i) identification of respective codons for all mutants (reported at the protein level) based on both minimum free energy and probabilistic approaches, (ii) rational design of siRNA, (iii) secondary structure analysis for the target accessibility of siRNA, (iii) determination of the ability of siRNA to interact with mRNA and the formation/stability of duplex via molecular dynamics study for a period of 15ns and (iv) characterization of mRNA-siRNA duplex stability based on thermo-physical analysis. The stable GC-rich siRNA expressed strong binding affinity towards mRNA and forms stable duplex in A-form. The linear dependence between the thermo-physical parameters such as Tm, GC content and binding free energy revealed the ability of the identified siRNAs to interact with mRNA in comparable to that of the experimentally reported siRNAs. Hence, this present study proposes few siRNAs as the possible gene silencing agents in RNAi therapy based on the in silico approach. PMID:26854610

  15. In Silico Risk Assessment of HLA-A*02:06-Associated Stevens-Johnson Syndrome and Toxic Epidermal Necrolysis Caused by Cold Medicine Ingredients

    PubMed Central

    Isogai, Hideto; Miyadera, Hiroko; Ueta, Mayumi; Sotozono, Chie; Kinoshita, Shigeru; Tokunaga, Katsushi

    2013-01-01

    Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN) are severe drug hypersensitivities with high mortality. Typical over-the-counter drugs of cold medicines are suggested to be causative. As multiple ingredients are generally contained in cold medicines, it is of particular interest to investigate which ingredients are responsible for SJS/TEN. However, experimental examination of causal relationships between SJS/TEN and a particular drug molecule is not straightforward. Significant association between HLA-A*02:06 and SJS/TEN with severe ocular surface complications has been observed in the Japanese. In the present study, we have undertaken in silico docking simulations between various ingredients contained in cold medicines available in Japan and the HLA-A*02:06 molecule. We use the composite risk index (CRI) that is the absolute value of the binding affinity multiplied by the daily dose to assess the potential risk of the adverse reactions. The drugs which have been recognized as causative drugs of SJS/TEN in Japan have revealed relatively high CRI, and the association between SJS/TEN and HLA-A*02:06 has been qualitatively verified. The results have also shown that some drugs whose links to SJS/TEN have not been clinically recognized in Japan show the high CRI and suggested that attention should be paid to their adverse drug reactions. PMID:24285954

  16. Designing and conducting in silico analysis for identifying of Echinococcus spp. with discrimination of novel haplotypes: an approach to better understanding of parasite taxonomic.

    PubMed

    Spotin, Adel; Gholami, Shirzad; Nasab, Abbas Najafi; Fallah, Esmaeil; Oskouei, Mahmoud Mahami; Semnani, Vahid; Shariatzadeh, Seyyed Ali; Shahbazi, Abbas

    2015-04-01

    The definitive identification of Echinococcus species is currently carried out by sequencing and phylogenetic strategies. However, the application of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) patterns is not broadly used as a result of heterogeneity traits of Echinococcus genome in different regions of the world. Therefore, designing and conducting a standardized pattern should indigenously be considered in under-studied areas. In this investigation, an in silico mapping was designed and developed for eight Echinococcus spp. on the basis of regional sequences in Iran and the world. The numbers of 60 Echinococcus isolates were collected from the liver and lungs of 15 human, 15 sheep, 15 cattle, and 15 camel cases in Semnan province, Central Iran. DNA samples were extracted and examined by polymerase chain reaction of ribosomal DNA (rDNA) internal transcribed spacer 1 (ITS1) and PCR-RFLP via Rsa1 endonuclease enzyme. Moreover, 15 amplicons of cytochrome oxidase 1 (Cox1) were directly sequenced in order to identify the strains/haplotypes. PCR-RFLP and phylogenetic analyses revealed firmly the presence of the G1 and G6 genotypes with heterogeneity (three novel haplotypes) of Cox1 gene although no other expected genotypes were found in the region. Finding shows that the identification of novel haplotypes along with discrimination of Echinococcus spp. through regional patterns can unambiguously illustrate the real taxonomic status of parasite in Central Iran. PMID:25645007

  17. PNA-COMBO-FISH: From combinatorial probe design in silico to vitality compatible, specific labelling of gene targets in cell nuclei.

    PubMed

    Müller, Patrick; Rößler, Jens; Schwarz-Finsterle, Jutta; Schmitt, Eberhard; Hausmann, Michael

    2016-07-01

    Recently, advantages concerning targeting specificity of PCR constructed oligonucleotide FISH probes in contrast to established FISH probes, e.g. BAC clones, have been demonstrated. These techniques, however, are still using labelling protocols with DNA denaturing steps applying harsh heat treatment with or without further denaturing chemical agents. COMBO-FISH (COMBinatorial Oligonucleotide FISH) allows the design of specific oligonucleotide probe combinations in silico. Thus, being independent from primer libraries or PCR laboratory conditions, the probe sequences extracted by computer sequence data base search can also be synthesized as single stranded PNA-probes (Peptide Nucleic Acid probes). Gene targets can be specifically labelled with at least about 20 PNA-probes obtaining visibly background free specimens. By using appropriately designed triplex forming oligonucleotides, the denaturing procedures can completely be omitted. These results reveal a significant step towards oligonucleotide-FISH maintaining the 3d-nanostructu