Sample records for identify biochemical pathways

  1. The jasmonate biochemical pathway.

    PubMed

    Liechti, Robin; Farmer, Edward E

    2003-10-01

    Plants possess an interrelated and interacting family of potent fatty acid-derived regulators--the jasmonates. These compounds, which play roles in both defense and development, are derived from tri-unsaturated fatty acids [alpha-linolenic acid (18:3) or 7Z,10Z,13Z-hexadecatrienoic acid (16:3)]. The lipoxygenase-catalyzed addition of molecular oxygen to alpha-linolenic acid initiates jasmonate synthesis by providing a 13-hydroperoxide substrate for the formation of an unstable allene oxide that is then subject to enzyme-guided cyclization to produce 12-oxo-phytodienoic acid (OPDA). OPDA, a key regulatory lipid in the plant immune system, has several fates, including esterification into plastid lipids or transformation into the 12-carbon co-regulator jasmonic acid (JA). JA, the best-characterized member of the family, regulates both male and female fertility (depending on the plant species), and is an important mediator of defense gene expresssion. JA is itself a substrate for further diverse modifications. Genetic dissection of the pathway is revealing how the different jasmonates modulate different physiological processes. Each new family member that is discovered provides another key to understanding the fine control of gene expression in immune responses, in the initiation and maintenance of long-distance signal transfer in response to wounding, and in the regulation of fertility, among other processes. The Jasmonate Biochemical Pathway provides an overview of the growing jasmonate family, and new members will be included in future versions of the Connections Map. Science Viewpoint R. Liechti, E. E. Farmer, The jasmonate pathway. Science 296, 1649-1650 (2002). [Abstract] [Full Text] PMID:14534325

  2. "Which Pathway Am I?" Using a Game Approach to Teach Students about Biochemical Pathways

    ERIC Educational Resources Information Center

    Ooi, Beng Guat; Sanger, Michael J.

    2009-01-01

    This game was designed to provide students with an alternative way to learn biochemical pathways through an interactive approach. In this game, students worked in pairs to help each other identify pathways taped to each other's backs by asking simple "yes or no" questions related to these pathways. This exercise was conducted after the traditional…

  3. The Neutral Sphingomyelinase Family: Identifying Biochemical Connections

    PubMed Central

    Clarke, Christopher J.; Wu, Bill X.; Hannun, Yusuf A.

    2010-01-01

    Neutral sphingomyelinases (N-SMases) are considered to be key mediators of stress-induced ceramide production. The extended family of N-SMases is a subset of the DNaseI superfamily and comprises members from bacteria, yeast and mammals. In recent years, the identification and cloning of mammalian N-SMase family members has led to significant advances in understanding their physiological roles and regulation. However, there is still limited information on their regulation at the biochemical and molecular level. In this review, we summarize current knowledge about the biochemical regulation of the eukaryotic N-SMases and identify the major areas where knowledge is lacking. PMID:21035485

  4. Biochemical Pathway of Stress-induced Ethylene

    PubMed Central

    Abeles, A. L.; Abeles, F. B.

    1972-01-01

    Ethylene production from beam and tobacco leaves increased rapidly following the application of toxic compounds such as CuSO4, Endothal, and ozone. Treatments which increased ethylene evolution also increased the conversion of U-14C-methionine into ethylene. Cycloheximide inhibited the production of chemical stress-induced ethylene. These results suggest that ethylene is produced by the same biochemical pathway forming basal ethylene, auxin-induced ethylene, or that produced during the ripening of climacteric fruit. PMID:16658203

  5. Identifying biochemical phenotypic differences between cryptic species.

    PubMed

    Liebeke, Manuel; Bruford, Michael W; Donnelly, Robert K; Ebbels, Timothy M D; Hao, Jie; Kille, Peter; Lahive, Elma; Madison, Rachael M; Morgan, A John; Pinto-Juma, Gabriela A; Spurgeon, David J; Svendsen, Claus; Bundy, Jacob G

    2014-09-01

    Molecular genetic methods can distinguish divergent evolutionary lineages in what previously appeared to be single species, but it is not always clear what functional differences exist between such cryptic species. We used a metabolomic approach to profile biochemical phenotype (metabotype) differences between two putative cryptic species of the earthworm Lumbricus rubellus. There were no straightforward metabolite biomarkers of lineage, i.e. no metabolites that were always at higher concentration in one lineage. Multivariate methods, however, identified a small number of metabolites that together helped distinguish the lineages, including uncommon metabolites such as N?-trimethyllysine, which is not usually found at high concentrations. This approach could be useful for characterizing functional trait differences, especially as it is applicable to essentially any species group, irrespective of its genome sequencing status. PMID:25252836

  6. Weighting schemes in metabolic graphs for identifying biochemical routes.

    PubMed

    Ghosh, S; Baloni, P; Vishveshwara, S; Chandra, N

    2014-03-01

    Metabolism forms an integral part of all cells and its study is important to understand the functioning of the system, to understand alterations that occur in disease state and hence for subsequent applications in drug discovery. Reconstruction of genome-scale metabolic graphs from genomics and other molecular or biochemical data is now feasible. Few methods have also been reported for inferring biochemical pathways from these networks. However, given the large scale and complex inter-connections in the networks, the problem of identifying biochemical routes is not trivial and some questions still remain open. In particular, how a given path is altered in perturbed conditions remains a difficult problem, warranting development of improved methods. Here we report a comparison of 6 different weighting schemes to derive node and edge weights for a metabolic graph, weights reflecting various kinetic, thermodynamic parameters as well as abundances inferred from transcriptome data. Using a network of 50 nodes and 107 edges of carbohydrate metabolism, we show that kinetic parameter derived weighting schemes [Formula: see text] fare best. However, these are limited by their extent of availability, highlighting the usefulness of omics data under such conditions. Interestingly, transcriptome derived weights yield paths with best scores, but are inadequate to discriminate the theoretical paths. The method is tested on a system of Escherichia coli stress response. The approach illustrated here is generic in nature and can be used in the analysis for metabolic network from any species and perhaps more importantly for comparing condition-specific networks. PMID:24592291

  7. Identifying Branched Metabolic Pathways by Merging Linear Metabolic Pathways

    NASA Astrophysics Data System (ADS)

    Heath, Allison P.; Bennett, George N.; Kavraki, Lydia E.

    This paper presents a graph-based algorithm for identifying complex metabolic pathways in multi-genome scale metabolic data. These complex pathways are called branched pathways because they can arrive at a target compound through combinations of pathways that split compounds into smaller ones, work in parallel with many compounds, and join compounds into larger ones. While most previous work has focused on identifying linear metabolic pathways, branched metabolic pathways predominate in metabolic networks. Automatic identification of branched pathways has a number of important applications in areas that require deeper understanding of metabolism, such as metabolic engineering and drug target identification. Our algorithm utilizes explicit atom tracking to identify linear metabolic pathways and then merges them together into branched metabolic pathways. We provide results on two well-characterized metabolic pathways that demonstrate that this new merging approach can efficiently find biologically relevant branched metabolic pathways with complex structures.

  8. Identifying Branched Metabolic Pathways by Merging Linear Metabolic Pathways

    E-print Network

    Kavraki, Lydia E.

    applications in fields such as metabolic engineering, which focuses on discovering and implementing newIdentifying Branched Metabolic Pathways by Merging Linear Metabolic Pathways Allison P. Heath1 presents a graph-based algorithm for identify- ing complex metabolic pathways in multi-genome scale

  9. Construction and engineering of large biochemical pathways via DNA assembler

    PubMed Central

    Shao, Zengyi; Zhao, Huimin

    2015-01-01

    Summary DNA assembler enables rapid construction and engineering of biochemical pathways in a one-step fashion by exploitation of the in vivo homologous recombination mechanism in Saccharomyces cerevisiae. It has many applications in pathway engineering, metabolic engineering, combinatorial biology, and synthetic biology. Here we use two examples including the zeaxanthin biosynthetic pathway and the aureothin biosynthetic gene cluster to describe the key steps in the construction of pathways containing multiple genes using the DNA assembler approach. Methods for construct design, pathway assembly, pathway confirmation, and functional analysis are shown. The protocol for fine genetic modifications such as site-directed mutagenesis for engineering the aureothin gene cluster is also illustrated. PMID:23996442

  10. Identifying optimal models to represent biochemical systems.

    PubMed

    Apri, Mochamad; de Gee, Maarten; van Mourik, Simon; Molenaar, Jaap

    2014-01-01

    Biochemical systems involving a high number of components with intricate interactions often lead to complex models containing a large number of parameters. Although a large model could describe in detail the mechanisms that underlie the system, its very large size may hinder us in understanding the key elements of the system. Also in terms of parameter identification, large models are often problematic. Therefore, a reduced model may be preferred to represent the system. Yet, in order to efficaciously replace the large model, the reduced model should have the same ability as the large model to produce reliable predictions for a broad set of testable experimental conditions. We present a novel method to extract an "optimal" reduced model from a large model to represent biochemical systems by combining a reduction method and a model discrimination method. The former assures that the reduced model contains only those components that are important to produce the dynamics observed in given experiments, whereas the latter ensures that the reduced model gives a good prediction for any feasible experimental conditions that are relevant to answer questions at hand. These two techniques are applied iteratively. The method reveals the biological core of a model mathematically, indicating the processes that are likely to be responsible for certain behavior. We demonstrate the algorithm on two realistic model examples. We show that in both cases the core is substantially smaller than the full model. PMID:24416170

  11. A biochemical approach to identifying microRNA targets

    PubMed Central

    Karginov, Fedor V.; Conaco, Cecilia; Xuan, Zhenyu; Schmidt, Bryan H.; Parker, Joel S.; Mandel, Gail; Hannon, Gregory J.

    2007-01-01

    Identifying the downstream targets of microRNAs (miRNAs) is essential to understanding cellular regulatory networks. We devised a direct biochemical method for miRNA target discovery that combined RNA-induced silencing complex (RISC) purification with microarray analysis of bound mRNAs. Because targets of miR-124a have been analyzed, we chose it as our model. We honed our approach both by examining the determinants of stable binding between RISC and synthetic target RNAs in vitro and by determining the dependency of both repression and RISC coimmunoprecipitation on miR-124a seed sites in two of its well characterized targets in vivo. Examining the complete spectrum of miR-124 targets in 293 cells yielded both a set that were down-regulated at the mRNA level, as previously observed, and a set whose mRNA levels were unaffected by miR-124a. Reporter assays validated both classes, extending the spectrum of mRNA targets that can be experimentally linked to the miRNA pathway. PMID:18042700

  12. A biochemical approach to identifying microRNA targets.

    PubMed

    Karginov, Fedor V; Conaco, Cecilia; Xuan, Zhenyu; Schmidt, Bryan H; Parker, Joel S; Mandel, Gail; Hannon, Gregory J

    2007-12-01

    Identifying the downstream targets of microRNAs (miRNAs) is essential to understanding cellular regulatory networks. We devised a direct biochemical method for miRNA target discovery that combined RNA-induced silencing complex (RISC) purification with microarray analysis of bound mRNAs. Because targets of miR-124a have been analyzed, we chose it as our model. We honed our approach both by examining the determinants of stable binding between RISC and synthetic target RNAs in vitro and by determining the dependency of both repression and RISC coimmunoprecipitation on miR-124a seed sites in two of its well characterized targets in vivo. Examining the complete spectrum of miR-124 targets in 293 cells yielded both a set that were down-regulated at the mRNA level, as previously observed, and a set whose mRNA levels were unaffected by miR-124a. Reporter assays validated both classes, extending the spectrum of mRNA targets that can be experimentally linked to the miRNA pathway. PMID:18042700

  13. Parameter identifiability of power-law biochemical system models.

    PubMed

    Srinath, Sridharan; Gunawan, Rudiyanto

    2010-09-01

    Mathematical modeling has become an integral component in biotechnology, in which these models are frequently used to design and optimize bioprocesses. Canonical models, like power-laws within the Biochemical Systems Theory, offer numerous mathematical and numerical advantages, including built-in flexibility to simulate general nonlinear behavior. The construction of such models relies on the estimation of unknown case-specific model parameters by way of experimental data fitting, also known as inverse modeling. Despite the large number of publications on this topic, this task remains the bottleneck in canonical modeling of biochemical systems. The focus of this paper concerns with the question of identifiability of power-law models from dynamic data, that is, whether the parameter values can be uniquely and accurately identified from time-series data. Existing and newly developed parameter identifiability methods were applied to two power-law models of biochemical systems, and the results pointed to the lack of parametric identifiability as the root cause of the difficulty faced in the inverse modeling. Despite the focus on power-law models, the analyses and conclusions are extendable to other canonical models, and the issue of parameter identifiability is expected to be a common problem in biochemical system modeling. PMID:20197073

  14. AraCyc: A Biochemical Pathway Database for Arabidopsis1

    PubMed Central

    Mueller, Lukas A.; Zhang, Peifen; Rhee, Seung Y.

    2003-01-01

    AraCyc is a database containing biochemical pathways of Arabidopsis, developed at The Arabidopsis Information Resource (http://www.arabidopsis.org). The aim of AraCyc is to represent Arabidopsis metabolism as completely as possible with a user-friendly Web-based interface. It presently features more than 170 pathways that include information on compounds, intermediates, cofactors, reactions, genes, proteins, and protein subcellular locations. The database uses Pathway Tools software, which allows the users to visualize a bird's eye view of all pathways in the database down to the individual chemical structures of the compounds. The database was built using Pathway Tools' Pathologic module with MetaCyc, a collection of pathways from more than 150 species, as a reference database. This initial build was manually refined and annotated. More than 20 plant-specific pathways, including carotenoid, brassinosteroid, and gibberellin biosyntheses have been added from the literature. A list of more than 40 plant pathways will be added in the coming months. The quality of the initial, automatic build of the database was compared with the manually improved version, and with EcoCyc, an Escherichia coli database using the same software system that has been manually annotated for many years. In addition, a Perl interface, PerlCyc, was developed that allows programmers to access Pathway Tools databases from the popular Perl language. AraCyc is available at the tools section of The Arabidopsis Information Resource Web site (http://www.arabidopsis.org/tools/aracyc). PMID:12805578

  15. Genetic and Biochemical Analysis of the SLN1 Pathway in Saccharomyces cerevisiae

    PubMed Central

    West, Ann H.

    2010-01-01

    The histidine kinase based signal transduction pathway was first uncovered in bacteria and is a prominent form of regulation in prokaryotes. However, this type of signal transduction is not unique to prokaryotes; over the last decade two-component signal transduction pathways have been identified and characterized in diverse eukaryotes, from unicellular yeasts to multicellular land plants. A number of small but important differences have been noted in the architecture and function of eukaryotic pathways. Because of the powerful genetic approaches and facile molecular analysis associated with the yeast system, the SLN1 osmotic response pathway in S. cerevisiae is particularly useful as a eukaryotic pathway model. This chapter provides an overview of genetic and biochemical methods that have been important in elucidating the stimulus-response events that underlie this pathway and in understanding the details of a eukaryotic His-Asp phosphorelay. PMID:20946854

  16. Computational tools for the synthetic design of biochemical pathways

    Microsoft Academic Search

    Marnix H. Medema; Renske van Raaphorst; Rainer Breitling; Eriko Takano

    2012-01-01

    As the field of synthetic biology is developing, the prospects for de novo design of biosynthetic pathways are becoming more and more realistic. Hence, there is an increasing need for computational tools that can support these efforts. A range of algorithms has been developed that can be used to identify all possible metabolic pathways and their corresponding enzymatic parts. These

  17. An algebraic-combinatorial model for the identification and mapping of biochemical pathways.

    PubMed

    Oliveira, J S; Bailey, C G; Jones-Oliveira, J B; Dixon, D A

    2001-11-01

    We develop the mathematical machinery for the construction of an algebraic-combinatorial model using Petri nets to construct an oriented matroid representation of biochemical pathways. For demonstration purposes, we use a model metabolic pathway example from the literature to derive a general biochemical reaction network model. The biomolecular networks define a connectivity matrix that identifies a linear representation of a Petri net. The sub-circuits that span a reaction network are subject to flux conservation laws. The conservation laws correspond to algebraic-combinatorial dual invariants, that are called S- (state) and T- (transition) invariants. Each invariant has an associated minimum support. We show that every minimum support of a Petri net invariant defines a unique signed sub-circuit representation. We prove that the family of signed sub-circuits has an implicit order that defines an oriented matroid. The oriented matroid is then used to identify the feasible sub-circuit pathways that span the biochemical network as the positive cycles in a hyper-digraph. PMID:11732180

  18. Biochemical pathway and degradation of phthalate ester isomers by bacteria.

    PubMed

    Gu, J D; Li, J; Wang, Y

    2005-01-01

    Degradation of dimethyl isophthalate (DMI) and dimethyl phthalate ester (DMPE) was investigated using microorganisms isolated from mangrove sediment of Hong Kong Mai Po Nature Reserve. One enrichment culture was capable of utilizing DMI as the sole source of carbon and energy, but none of the bacteria in the enrichment culture was capable of degrading DMI alone. In co-culture of two bacteria, degradation was observed proceeding through monomethyl isophthalate (MMI) ester and isophthalic acid (IPA) before the aromatic ring opening. Using DMI as the sole carbon and energy source, Klebsiella oxytoca Sc and Methylobacterium mesophilicum Sr degraded DMI through the biochemical cooperation. The initial hydrolytic reaction of the ester bond was by K. oxytoca Sc and the next step of transformation was by M. mesophilicum Sr, and IPA was degraded by both of them. In another investigation, a novel bacterium, strain MPsc, was isolated for degradation of dimethyl phthalate ester (DMPE) also from the mangrove sediment. On the basis of phenotypic, biochemical and 16S rDNA gene sequence analyses, the strain MPsc should be considered as a new bacterium at the genus level (8% differences). This strain, together with a Rhodococcus zopfii isolated from the same mangrove sediment, was able to degrade DMPE aerobically. The consortium consisting of the two species degraded 450 mg/l DMPE within 3 days as the sole source of carbon and energy, but none of the individual species alone was able to transform DMPE. Furthermore, the biochemical degradation pathway proceeded through monomethyl phthalate (MMP), phthalic acid (PA) and then protocatechuate before aromatic ring cleavage. Our results suggest that degradation of complex organic compounds including DMI and DMPE may be carried out by several members of microorganisms working together in the natural environments. PMID:16312973

  19. Using the Biochemical Pathway Model To Teach the Concepts of Gene Interaction and Epistasis.

    ERIC Educational Resources Information Center

    Chinnici, Joseph P.

    1999-01-01

    Describes the successful use of giving examples of genes affecting various steps in biochemical pathways to teach gene interaction. Finds that once students grasp the notion that genes can interact because they control different steps within biochemical pathways, the reason why phenotypic ratios appear to be non-Mendelian becomes more obvious and…

  20. Characterization of Changes in Gene Expression and Biochemical Pathways at Low Levels of Benzene Exposure

    PubMed Central

    Thomas, Reuben; Hubbard, Alan E.; McHale, Cliona M.; Zhang, Luoping; Rappaport, Stephen M.; Lan, Qing; Rothman, Nathaniel; Vermeulen, Roel; Guyton, Kathryn Z.; Jinot, Jennifer; Sonawane, Babasaheb R.; Smith, Martyn T.

    2014-01-01

    Benzene, a ubiquitous environmental pollutant, causes acute myeloid leukemia (AML). Recently, through transcriptome profiling of peripheral blood mononuclear cells (PBMC), we reported dose-dependent effects of benzene exposure on gene expression and biochemical pathways in 83 workers exposed across four airborne concentration ranges (from <1 ppm to >10 ppm) compared with 42 subjects with non-workplace ambient exposure levels. Here, we further characterize these dose-dependent effects with continuous benzene exposure in all 125 study subjects. We estimated air benzene exposure levels in the 42 environmentally-exposed subjects from their unmetabolized urinary benzene levels. We used a novel non-parametric, data-adaptive model selection method to estimate the change with dose in the expression of each gene. We describe non-parametric approaches to model pathway responses and used these to estimate the dose responses of the AML pathway and 4 other pathways of interest. The response patterns of majority of genes as captured by mean estimates of the first and second principal components of the dose-response for the five pathways and the profiles of 6 AML pathway response-representative genes (identified by clustering) exhibited similar apparent supra-linear responses. Responses at or below 0.1 ppm benzene were observed for altered expression of AML pathway genes and CYP2E1. Together, these data show that benzene alters disease-relevant pathways and genes in a dose-dependent manner, with effects apparent at doses as low as 100 ppb in air. Studies with extensive exposure assessment of subjects exposed in the low-dose range between 10 ppb and 1 ppm are needed to confirm these findings. PMID:24786086

  1. Unraveling biochemical pathways affected by mitochondrial dysfunctions using metabolomic approaches.

    PubMed

    Demine, Stéphane; Reddy, Nagabushana; Renard, Patricia; Raes, Martine; Arnould, Thierry

    2014-01-01

    Mitochondrial dysfunction(s) (MDs) can be defined as alterations in the mitochondria, including mitochondrial uncoupling, mitochondrial depolarization, inhibition of the mitochondrial respiratory chain, mitochondrial network fragmentation, mitochondrial or nuclear DNA mutations and the mitochondrial accumulation of protein aggregates. All these MDs are known to alter the capacity of ATP production and are observed in several pathological states/diseases, including cancer, obesity, muscle and neurological disorders. The induction of MDs can also alter the secretion of several metabolites, reactive oxygen species production and modify several cell-signalling pathways to resolve the mitochondrial dysfunction or ultimately trigger cell death. Many metabolites, such as fatty acids and derived compounds, could be secreted into the blood stream by cells suffering from mitochondrial alterations. In this review, we summarize how a mitochondrial uncoupling can modify metabolites, the signalling pathways and transcription factors involved in this process. We describe how to identify the causes or consequences of mitochondrial dysfunction using metabolomics (liquid and gas chromatography associated with mass spectrometry analysis, NMR spectroscopy) in the obesity and insulin resistance thematic. PMID:25257998

  2. Comparing Transcription Rate and mRNA Abundance as Parameters for Biochemical Pathway and Network Analysis

    Microsoft Academic Search

    Brewster Hayles; Sailu Yellaboina; Degeng Wang

    2010-01-01

    The cells adapt to extra- and intra-cellular signals by dynamic orchestration of activities of pathways in the biochemical networks. Dynamic control of the gene expression process represents a major mechanism for pathway activity regulation. Gene expression has thus been routinely measured, most frequently at steady-state mRNA abundance level using micro-array technology. The results are widely used in statistical inference of

  3. Metabolic PathFinding: inferring relevant pathways in biochemical networks.

    PubMed

    Croes, Didier; Couche, Fabian; Wodak, Shoshana J; van Helden, Jacques

    2005-07-01

    Our knowledge of metabolism can be represented as a network comprising several thousands of nodes (compounds and reactions). Several groups applied graph theory to analyse the topological properties of this network and to infer metabolic pathways by path finding. This is, however, not straightforward, with a major problem caused by traversing irrelevant shortcuts through highly connected nodes, which correspond to pool metabolites and co-factors (e.g. H2O, NADP and H+). In this study, we present a web server implementing two simple approaches, which circumvent this problem, thereby improving the relevance of the inferred pathways. In the simplest approach, the shortest path is computed, while filtering out the selection of highly connected compounds. In the second approach, the shortest path is computed on the weighted metabolic graph where each compound is assigned a weight equal to its connectivity in the network. This approach significantly increases the accuracy of the inferred pathways, enabling the correct inference of relatively long pathways (e.g. with as many as eight intermediate reactions). Available options include the calculation of the k-shortest paths between two specified seed nodes (either compounds or reactions). Multiple requests can be submitted in a queue. Results are returned by email, in textual as well as graphical formats (available in http://www.scmbb.ulb.ac.be/pathfinding/). PMID:15980483

  4. Genetic and Biochemical Characterization of the Pathway in Pantoea citrea Leading to Pink Disease of Pineapple

    Microsoft Academic Search

    CATHERINE J. PUJOL; CLARENCE I. KADO

    2000-01-01

    Pink disease of pineapple, caused by Pantoea citrea, is characterized by a dark coloration on fruit slices after autoclaving. This coloration is initiated by the oxidation of glucose to gluconate, which is followed by further oxidation of gluconate to as yet unknown chromogenic compounds. To elucidate the biochemical pathway leading to pink disease, we generated six coloration-defective mutants of P.

  5. Biochemical Pathways in Prokaryotes Can Be Traced Backward through Evolutionary Time

    Microsoft Academic Search

    Roy A. Jensen

    1985-01-01

    For the first time, a credible prokaryotic phylogenetic tree is being assembled by Woese and others using quantitative sequence analysis of oligonucleotides in the highly conservative rRNA. This provides an evolutionary scale against which the evolutionary steps that led to the arrangement and regulation of contemporary biochemical pathways can be measured. This paper presents an emerging evolutionary picture of aromatic

  6. Using biologically interrelated experiments to identify pathway genes in Arabidopsis

    PubMed Central

    Kim, Kyungpil; Jiang, Keni; Teng, Siew Leng; Feldman, Lewis J.; Huang, Haiyan

    2012-01-01

    Motivation: Pathway genes are considered as a group of genes that work cooperatively in the same pathway constituting a fundamental functional grouping in a biological process. Identifying pathway genes has been one of the major tasks in understanding biological processes. However, due to the difficulty in characterizing/inferring different types of biological gene relationships, as well as several computational issues arising from dealing with high-dimensional biological data, deducing genes in pathways remain challenging. Results: In this work, we elucidate higher level gene–gene interactions by evaluating the conditional dependencies between genes, i.e. the relationships between genes after removing the influences of a set of previously known pathway genes. These previously known pathway genes serve as seed genes in our model and will guide the detection of other genes involved in the same pathway. The detailed statistical techniques involve the estimation of a precision matrix whose elements are known to be proportional to partial correlations (i.e. conditional dependencies) between genes under appropriate normality assumptions. Likelihood ratio tests on two forms of precision matrices are further performed to see if a candidate pathway gene is conditionally independent of all the previously known pathway genes. When used effectively, this is a promising approach to recover gene relationships that would have otherwise been missed by standard methods. The advantage of the proposed method is demonstrated using both simulation studies and real datasets. We also demonstrated the importance of taking into account experimental dependencies in the simulation and real data studies. Contact: hhuang@stat.berkeley.edu; ljfeldman@berkeley.edu Supplementary information:Supplementary data are available at Bioinformatics online. PMID:22271267

  7. The biochemical pathways of central nervous system neural degeneration in niacin deficiency

    PubMed Central

    Fu, Linshan; Doreswamy, Venkatesh; Prakash, Ravi

    2014-01-01

    Neural degeneration is a very complicated process. In spite of all the advancements in the molecular chemistry, there are many unknown aspects of the phenomena of neurodegeneration which need to be put together. It is a common sequela of the conditions of niacin deficiency. Neural degeneration in Pellagra manifests as chromatolysis mainly in pyramidal followed by other neurons and glial cells. However, there is a gross lack of understanding of biochemical mechanisms of neurodegeneration in niacin deficiency states. Because of the necessity of niacin or its amide derivative NAD in a number of biochemical pathways, it is understandable that several of these pathways may be involved in the common outcome of neural degeneration. Here, we highlight five pathways that could be involved in the neuraldegeneration for which evidence has accumulated through several studies. These pathways are: 1) the tryptophan-kyneurenic acid pathway, 2) the mitochondrial ATP generation related pathways, 3) the poly (ADP-ibose) polymerase (PARP) pathway, 4) the BDNF-TRKB Axis abnormalities, 5) the genetic influences of niacin deficiency. PMID:25317166

  8. Identifying Differentially Abundant Metabolic Pathways in Metagenomic Datasets

    Microsoft Academic Search

    Bo Liu; Mihai Pop

    2010-01-01

    \\u000a Enabled by rapid advances in sequencing technology, metagenomic studies aim to characterize entire communities of microbes\\u000a bypassing the need for culturing individual bacterial members. One major goal of such studies is to identify specific functional\\u000a adaptations of microbial communities to their habitats. Here we describe a powerful analytical method (MetaPath) that can\\u000a identify differentially abundant pathways in metagenomic data-sets, relying

  9. Spatial Control of Biochemical Modification Cascades and Pathways.

    PubMed

    Alam-Nazki, Aiman; Krishnan, J

    2015-06-16

    Information transmission in cells occurs through complex networks of proteins and genes and is relayed through cascades of biochemical modifications, which are typically studied through ordinary differential equations. However, it is becoming increasingly clear that spatial factors can strongly influence chemical information transmission in cells. In this article, we systematically disentangle the effects of space in signaling cascades. This is done by examining the effects of localization/compartmentalization and diffusion of enzymes and substrates in multiple variants of chemical modification cascades. This includes situations where the modified form of species at one stage 1) acts as an enzyme for the next stage; 2) acts as a substrate for the next stage; and 3) is involved in phosphotransfer. Our analysis reveals the multiple effects of space in signal transduction cascades. Although in some cases space plays a modulatory effect (itself of interest), in other cases, spatial regulation and control can profoundly affect the nature of information processing as a result of the subtle interplay between the patterns of localization of species, diffusion, and the nature of the modification cascades. Our results provide a platform for disentangling the role of space and spatial control in multiple cellular contexts and a basis for engineering spatial control in signaling cascades through localization/compartmentalization. PMID:26083931

  10. AraCyc: A Biochemical Pathway Database for Arabidopsis1

    E-print Network

    Arabidopsis was the first plant genome to be fully sequenced (Arabidopsis Genome Initiative, 2000). Initially, ap- proximately 26,000 genes were identified in the genomic sequence, based on different contain the entire genomic informa- tion of an organism, including its metabolic com- pounds, reactions

  11. Structural and biochemical studies identify tobacco SABP2 as a methyl salicylate esterase and implicate

    E-print Network

    Pichersky, Eran

    Structural and biochemical studies identify tobacco SABP2 as a methyl salicylate esterase­20) to form methyl salicylate (MeSA) and SA -glucoside, respectively. These SA derivatives appear) Salicylic acid (SA) is a critical signal for the activation of plant defense responses against pathogen

  12. A Three Stage Integrative Pathway Search (TIPS©) framework to identify toxicity relevant genes and pathways

    PubMed Central

    Li, Zheng; Srivastava, Shireesh; Mittal, Sheenu; Yang, Xuerui; Sheng, Lufang; Chan, Christina

    2007-01-01

    Background The ability to obtain profiles of gene expressions, proteins and metabolites with the advent of high throughput technologies has advanced the study of pathway and network reconstruction. Genome-wide network reconstruction requires either interaction measurements or large amount of perturbation data, often not available for mammalian cell systems. To overcome these shortcomings, we developed a Three Stage Integrative Pathway Search (TIPS©) approach to reconstruct context-specific active pathways involved in conferring a specific phenotype, from limited amount of perturbation data. The approach was tested on human liver cells to identify pathways that confer cytotoxicity. Results This paper presents a systems approach that integrates gene expression and cytotoxicity profiles to identify a network of pathways involved in free fatty acid (FFA) and tumor necrosis factor-? (TNF-?) induced cytotoxicity in human hepatoblastoma cells (HepG2/C3A). Cytotoxicity relevant genes were first identified and then used to reconstruct a network using Bayesian network (BN) analysis. BN inference was used subsequently to predict the effects of perturbing a gene on the other genes in the network and on the cytotoxicity. These predictions were subsequently confirmed through the published literature and further experiments. Conclusion The TIPS© approach is able to reconstruct active pathways that confer a particular phenotype by integrating gene expression and phenotypic profiles. A web-based version of TIPS© that performs the analysis described herein can be accessed at . PMID:17570844

  13. Signal duration and the time scale dependence of signal integration in biochemical pathways

    E-print Network

    Jason W. Locasale

    2008-02-19

    Signal duration (e.g. the time scales over which an active signaling intermediate persists) is a key regulator of biological decisions in myriad contexts such as cell growth, proliferation, and developmental lineage commitments. Accompanying differences in signal duration are numerous downstream biological processes that require multiple steps of biochemical regulation. Here, we present an analysis that investigates how simple biochemical motifs that involve multiple stages of regulation can be constructed to differentially process signals that persist at different time scales. We compute the dynamic gain within these networks and resulting power spectra to better understand how biochemical networks can integrate signals at different time scales. We identify topological features of these networks that allow for different frequency dependent signal processing properties. Our studies suggest design principles for why signal duration in connection with multiple steps of downstream regulation is a ubiquitous control motif in biochemical systems.

  14. Metabolic control analysis of biochemical pathways based on a thermokinetic description of reaction rates.

    PubMed Central

    Nielsen, J

    1997-01-01

    Metabolic control analysis is a powerful technique for the evaluation of flux control within biochemical pathways. Its foundation is the elasticity coefficients and the flux control coefficients (FCCs). On the basis of a thermokinetic description of reaction rates it is here shown that the elasticity coefficients can be calculated directly from the pool levels of metabolites at steady state. The only requirement is that one thermodynamic parameter be known, namely the reaction affinity at the intercept of the tangent in the inflection point of the curve of reaction rate against reaction affinity. This parameter can often be determined from experiments in vitro. The methodology is applicable only to the analysis of simple two-step pathways, but in many cases larger pathways can be lumped into two overall conversions. In cases where this cannot be done it is necessary to apply an extension of the thermokinetic description of reaction rates to include the influence of effectors. Here the reaction rate is written as a linear function of the logarithm of the metabolite concentrations. With this type of rate function it is shown that the approach of Delgado and Liao [Biochem. J. (1992) 282, 919-927] can be much more widely applied, although it was originally based on linearized kinetics. The methodology of determining elasticity coefficients directly from pool levels is illustrated with an analysis of the first two steps of the biosynthetic pathway of penicillin. The results compare well with previous findings based on a kinetic analysis. PMID:9003411

  15. Diversity of bile salts in fish and amphibians: evolution of a complex biochemical pathway.

    PubMed

    Hagey, Lee R; Møller, Peter R; Hofmann, Alan F; Krasowski, Matthew D

    2010-01-01

    Bile salts are the major end metabolites of cholesterol and are also important in lipid and protein digestion, as well as shaping of the gut microflora. Previous studies had demonstrated variation of bile salt structures across vertebrate species. We greatly extend prior surveys of bile salt variation in fish and amphibians, particularly in analysis of the biliary bile salts of Agnatha and Chondrichthyes. While there is significant structural variation of bile salts across all fish orders, bile salt profiles are generally stable within orders of fish and do not correlate with differences in diet. This large data set allowed us to infer evolutionary changes in the bile salt synthetic pathway. The hypothesized ancestral bile salt synthetic pathway, likely exemplified in extant hagfish, is simpler and much shorter than the pathway of most teleost fish and terrestrial vertebrates. Thus, the bile salt synthetic pathway has become longer and more complex throughout vertebrate evolution. Analysis of the evolution of bile salt synthetic pathways provides a rich model system for the molecular evolution of a complex biochemical pathway in vertebrates. PMID:20113173

  16. Diversity of Bile Salts in Fish and Amphibians: Evolution of a Complex Biochemical Pathway

    PubMed Central

    Hagey, Lee R.; Møller, Peter R.; Hofmann, Alan F.; Krasowski, Matthew D.

    2010-01-01

    Bile salts are the major end-metabolites of cholesterol and are also important in lipid and protein digestion, as well as shaping of the gut microflora. Previous studies had demonstrated variation of bile salt structures across vertebrate species. We greatly extend prior surveys of bile salt variation in fish and amphibians, particularly in analysis of the biliary bile salts of Agnatha and Chondrichthyes. While there is significant structural variation of bile salts across all fish orders, bile salt profiles are generally stable within orders of fish and do not correlate with differences in diet. This large data set allowed us to infer evolutionary changes in the bile salt synthetic pathway. The hypothesized ancestral bile salt synthetic pathway, likely exemplified in extant hagfish, is simpler and much shorter than the pathway of most teleost fish and terrestrial vertebrates. Thus, the bile salt synthetic pathway has become longer and more complex throughout vertebrate evolution. Analysis of the evolution of bile salt synthetic pathways provides a rich model system for the molecular evolution of a complex biochemical pathway in vertebrates. PMID:20113173

  17. Structural and biochemical studies identify tobacco SABP2 as a methyl salicylate esterase and implicate it in plant innate immunity

    PubMed Central

    Forouhar, Farhad; Yang, Yue; Kumar, Dhirendra; Chen, Yang; Fridman, Eyal; Park, Sang Wook; Chiang, Yiwen; Acton, Thomas B.; Montelione, Gaetano T.; Pichersky, Eran; Klessig, Daniel F.; Tong, Liang

    2005-01-01

    Salicylic acid (SA) is a critical signal for the activation of plant defense responses against pathogen infections. We recently identified SA-binding protein 2 (SABP2) from tobacco as a protein that displays high affinity for SA and plays a crucial role in the activation of systemic acquired resistance to plant pathogens. Here we report the crystal structures of SABP2, alone and in complex with SA at up to 2.1-Å resolution. The structures confirm that SABP2 is a member of the ?/? hydrolase superfamily of enzymes, with Ser-81, His-238, and Asp-210 as the catalytic triad. SA is bound in the active site and is completely shielded from the solvent, consistent with the high affinity of this compound for SABP2. Our biochemical studies reveal that SABP2 has strong esterase activity with methyl salicylate as the substrate, and that SA is a potent product inhibitor of this catalysis. Modeling of SABP2 with MeSA in the active site is consistent with all these biochemical observations. Our results suggest that SABP2 may be required to convert MeSA to SA as part of the signal transduction pathways that activate systemic acquired resistance and perhaps local defense responses as well. PMID:15668381

  18. 876 Biochemical Society Transactions (2013) Volume 41, part 4 RNAi pathways in the recognition of foreign RNA

    E-print Network

    Miska, Eric

    2013-01-01

    876 Biochemical Society Transactions (2013) Volume 41, part 4 RNAi pathways in the recognition for which RNAi (RNA interference) in response to exogenous triggers was shown experimentally and subsequently the molecular components of the RNAi pathway have been characterized in some detail. However

  19. Fourier transform infrared spectroscopic imaging identifies early biochemical markers of tissue damage

    NASA Astrophysics Data System (ADS)

    Varma, Vishal K.; Ohlander, Samuel; Nguyen, Peter; Vendryes, Christopher; Parthiban, Sujeeth; Hamilton, Blake; Wallis, M. Chad; Kajdacsy-Balla, Andre; Hannaford, Blake; Lendvay, Thomas; Hotaling, James M.; Walsh, Michael J.

    2014-03-01

    Fourier Transform Infrared (FT-IR) spectroscopic imaging can allow for the rapid imaging of tissue biochemistry in a label-free and non-perturbing fashion. With the rapid adoption of new minimally invasive surgery (MIS) technologies over the last 20 years, adequate skill to safely and effectively use these technologies may not be achieved and risk of undue physical pressure being placed on tissues is a concern. Previous work has demonstrated that a number of histological stains can detect tissue damage, however, this process requires the initiation and progression of a signaling cascade that results in the epitope of interest being expressed. We proposed to identify the early biochemical markers associated with physical tissue damage from applied forces, thus not requiring transcriptional and translational protein synthesis as traditional immunohistochemistry does. To demonstrate that FT-IR can measure biochemical changes in tissues that have undergone physical force, we took ex-vivo lamb's liver that had been freshly excised and applied varying levels of physical pressure (0kPa to 30kPa). Tissues were then formalin-fixed, paraffin-embedded, and sectioned on to glass for H and E staining to identify damage and on to an IR slide for FT-IR imaging. Regions of interest containing hepatocytes were identified and average FT-IR spectra were extracted from the damaged and undamaged livers. FT-IR spectra showed clear biochemical changes associated with tissue damage. In addition, chemical changes could be observed proceeding histological changes observed when using conventional staining approaches.

  20. MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity

    PubMed Central

    2012-01-01

    Background Exposure to environmental tobacco smoke (ETS) leads to higher rates of pulmonary diseases and infections in children. To study the biochemical changes that may precede lung diseases, metabolomic effects on fetal and maternal lungs and plasma from rats exposed to ETS were compared to filtered air control animals. Genome- reconstructed metabolic pathways may be used to map and interpret dysregulation in metabolic networks. However, mass spectrometry-based non-targeted metabolomics datasets often comprise many metabolites for which links to enzymatic reactions have not yet been reported. Hence, network visualizations that rely on current biochemical databases are incomplete and also fail to visualize novel, structurally unidentified metabolites. Results We present a novel approach to integrate biochemical pathway and chemical relationships to map all detected metabolites in network graphs (MetaMapp) using KEGG reactant pair database, Tanimoto chemical and NIST mass spectral similarity scores. In fetal and maternal lungs, and in maternal blood plasma from pregnant rats exposed to environmental tobacco smoke (ETS), 459 unique metabolites comprising 179 structurally identified compounds were detected by gas chromatography time of flight mass spectrometry (GC-TOF MS) and BinBase data processing. MetaMapp graphs in Cytoscape showed much clearer metabolic modularity and complete content visualization compared to conventional biochemical mapping approaches. Cytoscape visualization of differential statistics results using these graphs showed that overall, fetal lung metabolism was more impaired than lungs and blood metabolism in dams. Fetuses from ETS-exposed dams expressed lower lipid and nucleotide levels and higher amounts of energy metabolism intermediates than control animals, indicating lower biosynthetic rates of metabolites for cell division, structural proteins and lipids that are critical for in lung development. Conclusions MetaMapp graphs efficiently visualizes mass spectrometry based metabolomics datasets as network graphs in Cytoscape, and highlights metabolic alterations that can be associated with higher rate of pulmonary diseases and infections in children prenatally exposed to ETS. The MetaMapp scripts can be accessed at http://metamapp.fiehnlab.ucdavis.edu. PMID:22591066

  1. Oxidation state, bioavailability & biochemical pathway define the fate of carbon in soil

    NASA Astrophysics Data System (ADS)

    Kuzyakov, Yakov; Apostel, Carolin; Gunina, Anna; Herrmann, Anke M.; Dippold, Michaela

    2015-04-01

    Numerous experiments under laboratory and field conditions analyzed microbial utilization and mean residence time (MRT) of carbon (C) from plant and microbial residues as well as root exudates in soil. Most of these studies tested the effects of various environmental factors, such as temperature, soil moisture, texture etc. on these parameters. However, only a few studies compared the properties of the substances themselves and there is no conceptual framework based on biochemical pathways. We hypothesize that the fate of C from organic substances in soil strongly depends on the first step of their microbial utilization, specifically, on biochemical pathway and initial C oxidation state, as well as its bioavailability in soils, defined by its hydrophobicity and molecular weight. Here we introduce and evaluate a new conceptual framework based on the following parameters: 1) C oxidation state, 2) molecular weight and hydrophobicity, 3) initial biochemical pathway of a substance class in microbial cells. To assess these parameters, two databases were prepared based on the literature and own studies. The first database included only the studies with 14C or 13C position specific labeled sugars, amino acids, carboxylic acids, phenols and lipids in soil. This database allowed us to analyze microbial utilization and mineralization of organics to CO2 depending on their C oxidation state (OS) and on functional groups. Additionally, we calculated data on the bond electronegativity of all compounds investigated in these studies. The second data base included the results of 14C and 13C studies with uniformly labeled substances of various classes. This database considered the free enthalpie (Delta H) per C unit from a variety of substrates differing in their aromaticity, hydrophobicity/electronegativity and location of the substance on the van Krevelen diagram. In addition, we calculated the hydrophobicity from the electronegativity of the individual bonds and recorded their molecular weight in our databases. For both data bases the decomposition rates and the MRT of C remaining in soil were calculated by the double first-order kinetics and related to the four parameter groups. The first database showed high correlation of mineralization rates to CO2 with the C oxidation state and biochemical pathway. Carboxyl group (OS = +3) was split at first from the skeleton of nearly all substances. In contrast, the methyl group (OS = -3) was mineralized as the slowest and after incorporation into microbial cells remained the longest period in soil. This general pattern reflects a clear preferential oxidation of already highly oxidized, polar functional groups. The initial use of substances within glucolysis (e.g. sugars) lead to a higher portion of remaining C in soil compared to C introduced via citric acid cycle (e.g. carboxylic acids). Concerning substance groups, the mineralization rates were the fastest for amino acids and sugars and the slowest for of the lipids - corresponding to their molecular weight and hydropobicity. This corresponded well with localization of the substance classes on the van Krevelen diagram. Generally, high oxidation state of the initial substance and consequently its low free enthalpy content lead to faster decomposition. In contrast, low oxidation state (e.g. lipids, aromatics) corresponds to high hydrophobicity and so, slow uptake from soil solution and utilization within microbial cells. Consequently, the optimum for microbial biomass utilization in soil and use for anabolic processes is common for sugars that have the oxidation state close to 0, have medium energy content and are hydrophilic. We conclude that from the tested substance properties, the oxidation state and biochemical pathway explained well the initial fate of C in soil, i.e. its mineralization to CO2 and incorporation into microbial biomass. Because the first step and microbial cycling are crucial for its further transformations, the same criteria are pivotal for C stabilization in soil.

  2. A systems biology approach to identify molecular pathways altered by HDAC inhibition in osteosarcoma.

    PubMed

    Wittenburg, Luke A; Ptitsyn, Andrey A; Thamm, Douglas H

    2012-03-01

    Osteosarcoma (OS) is the most common primary tumor in humans and dogs affecting the skeleton, and spontaneously occurring OS in dogs serves as an extremely useful model. Unacceptable toxicities using current treatment protocols prevent further dose-intensification from being a viable option to improve patient survival and thus, novel treatment strategies must be developed. Histone deacetylase inhibitors (HDACi) have recently emerged as a promising class of therapeutics demonstrating an ability to enhance the anti-tumor activity of traditional chemotherapeutics. To date, gene expression analysis of OS cell lines treated with HDACi has not been reported, and evaluation of the resultant gene expression changes may provide insight into the mechanisms that lead to success of HDACi. Canine OS cells, treated with a clinically relevant concentration of the HDACi valproic acid (VPA), were used for expression analysis on the Affymetrix canine v2.0 genechip. Differentially expressed genes were grouped into pathways based upon functional annotation; pathway analysis was performed with MetaCore and Ingenuity Pathways Analysis software. Validation of microarray results was performed by a combination of qRT-PCR and functional/biochemical assays revealing oxidative phosphorylation, cytoskeleton remodeling, cell cycle, and ubiquitin-proteasome among those pathways most affected by HDACi. The mitomycin C-bioactivating enzyme NQ01 also demonstrated upregulation following VPA treatment, leading to synergistic reductions in cell viability. These results provide a better understanding of the mechanisms by which HDACi exert their effect in OS, and have the potential to identify biomarkers that may serve as novel targets and/or predictors of response to HDACi-containing combination therapies in OS. PMID:21976144

  3. De novo assembly of Euphorbia fischeriana root transcriptome identifies prostratin pathway related genes

    PubMed Central

    2011-01-01

    Background Euphorbia fischeriana is an important medicinal plant found in Northeast China. The plant roots contain many medicinal compounds including 12-deoxyphorbol-13-acetate, commonly known as prostratin that is a phorbol ester from the tigliane diterpene series. Prostratin is a protein kinase C activator and is effective in the treatment of Human Immunodeficiency Virus (HIV) by acting as a latent HIV activator. Latent HIV is currently the biggest limitation for viral eradication. The aim of this study was to sequence, assemble and annotate the E. fischeriana transcriptome to better understand the potential biochemical pathways leading to the synthesis of prostratin and other related diterpene compounds. Results In this study we conducted a high throughput RNA-seq approach to sequence the root transcriptome of E. fischeriana. We assembled 18,180 transcripts, of these the majority encoded protein-coding genes and only 17 transcripts corresponded to known RNA genes. Interestingly, we identified 5,956 protein-coding transcripts with high similarity (> = 75%) to Ricinus communis, a close relative to E. fischeriana. We also evaluated the conservation of E. fischeriana genes against EST datasets from the Euphorbeacea family, which included R. communis, Hevea brasiliensis and Euphorbia esula. We identified a core set of 1,145 gene clusters conserved in all four species and 1,487 E. fischeriana paralogous genes. Furthermore, we screened E. fischeriana transcripts against an in-house reference database for genes implicated in the biosynthesis of upstream precursors to prostratin. This identified 24 and 9 candidate transcripts involved in the terpenoid and diterpenoid biosyntehsis pathways, respectively. The majority of the candidate genes in these pathways presented relatively low expression levels except for 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase (HDS) and isopentenyl diphosphate/dimethylallyl diphosphate synthase (IDS), which are required for multiple downstream pathways including synthesis of casbene, a proposed precursor to prostratin. Conclusion The resources generated in this study provide new insights into the upstream pathways to the synthesis of prostratin and will likely facilitate functional studies aiming to produce larger quantities of this compound for HIV research and/or treatment of patients. PMID:22151917

  4. Biochemical analysis on the parallel pathways of methionine biosynthesis in Corynebacterium glutamicum.

    PubMed

    Hwang, Byung-Joon; Park, Soo-Dong; Kim, Younhee; Kim, Pil; Lee, Heung-Shick

    2007-06-01

    Two alternative pathways for methionine biosynthesis are known in Corynebacterium glutamicum: one involving transsulfuration (mediated by metB and metC) and the other involving direct sulthydrylation (mediated by metY). In this study, MetB (cystathionine gamma-synthase) and MetY (O-acetylhomoserine sulfhydrylase) from C. glutamicum were purified to homogeneity and the biochemical parameters were compared to assess the functional and evolutionary importance of each pathway. The molecular masses of the native MetB and MetY proteins were measured to be approximately 170 and 280 kDa, respectively, showing that MetB was a homotetramer of 40-kDa subunits and MetY was a homohexamer of 45-kDa subunits. The Km values for the O-acetylhomoserine catalysis effected by MetB and MetY were 3.9 and 6.4 mM, and the maximum catalysis rates were 7.4 (kcat = 21 s(-1)) and 6.0 (kcat=28 s(-1)) micromol mg(-1) min(-1), respectively. This suggests that both MetB and MetY can be comparably active in vivo. Nevertheless, the Km value for sulfide ions by MetY was 8.6 mM, which was too high, considering the physiological condition. Moreover, MetB was active at a broad range of temperatures (30 and 65 degrees C) and pH (6.5 and 10.0), as compared with MetY, which was active in a range from 30 to 45 degrees C and at pH values from 7.0 to 8.5. In addition, MetY was inhibited by methionine, but MetB was not. These biochemical data may provide insight on the role of the parallel pathways of methionine biosynthesis in C. glutamicum with regard to cell physiology and evolution. PMID:18050920

  5. Serum Metabolomic Profiling in Acute Alcoholic Hepatitis Identifies Multiple Dysregulated Pathways

    PubMed Central

    Rachakonda, Vikrant; Gabbert, Charles; Raina, Amit; Bell, Lauren N.; Cooper, Sara; Malik, Shahid; Behari, Jaideep

    2014-01-01

    Background and Objectives While animal studies have implicated derangements of global energy homeostasis in the pathogenesis of acute alcoholic hepatitis (AAH), the relevance of these findings to the development of human AAH remains unclear. Using global, unbiased serum metabolomics analysis, we sought to characterize alterations in metabolic pathways associated with severe AAH and identify potential biomarkers for disease prognosis. Methods This prospective, case-control study design included 25 patients with severe AAH and 25 ambulatory patients with alcoholic cirrhosis. Serum samples were collected within 24 hours of the index clinical encounter. Global, unbiased metabolomics profiling was performed. Patients were followed for 180 days after enrollment to determine survival. Results Levels of 234 biochemicals were altered in subjects with severe AAH. Random-forest analysis, principal component analysis, and integrated hierarchical clustering methods demonstrated that metabolomics profiles separated the two cohorts with 100% accuracy. Severe AAH was associated with enhanced triglyceride lipolysis, impaired mitochondrial fatty acid beta oxidation, and upregulated omega oxidation. Low levels of multiple lysolipids and related metabolites suggested decreased plasma membrane remodeling in severe AAH. While most measured bile acids were increased in severe AAH, low deoxycholate and glycodeoxycholate levels indicated intestinal dysbiosis. Several changes in substrate utilization for energy homeostasis were identified in severe AAH, including increased glucose consumption by the pentose phosphate pathway, altered tricarboxylic acid (TCA) cycle activity, and enhanced peptide catabolism. Finally, altered levels of small molecules related to glutathione metabolism and antioxidant vitamin depletion were observed in patients with severe AAH. Univariable logistic regression revealed 15 metabolites associated with 180-day survival in severe AAH. Conclusion Severe AAH is characterized by a distinct metabolic phenotype spanning multiple pathways. Metabolomics profiling revealed a panel of biomarkers for disease prognosis, and future studies are planned to validate these findings in larger cohorts of patients with severe AAH. PMID:25461442

  6. Prediction and Biochemical Demonstration of a Catabolic Pathway for the Osmoprotectant Proline Betaine

    PubMed Central

    Kumar, Ritesh; Zhao, Suwen; Vetting, Matthew W.; Wood, B. McKay; Sakai, Ayano; Cho, Kyuil; Solbiati, José; Almo, Steven C.; Sweedler, Jonathan V.; Jacobson, Matthew P.; Gerlt, John A.; Cronan, John E.

    2014-01-01

    ABSTRACT Through the use of genetic, enzymatic, metabolomic, and structural analyses, we have discovered the catabolic pathway for proline betaine, an osmoprotectant, in Paracoccus denitrificans and Rhodobacter sphaeroides. Genetic and enzymatic analyses showed that several of the key enzymes of the hydroxyproline betaine degradation pathway also function in proline betaine degradation. Metabolomic analyses detected each of the metabolic intermediates of the pathway. The proline betaine catabolic pathway was repressed by osmotic stress and cold stress, and a regulatory transcription factor was identified. We also report crystal structure complexes of the P. denitrificans HpbD hydroxyproline betaine epimerase/proline betaine racemase with l-proline betaine and cis-hydroxyproline betaine. PMID:24520058

  7. Biochemical Pathways: An Atlas of Biochemistry and Molecular Biology (edited by Gerhard Michal)

    NASA Astrophysics Data System (ADS)

    Voige, Reviewed By William H.

    2000-02-01

    For decades, a wall chart detailing living organisms' metabolic pathways has been a fixture in many classrooms and laboratories where biochemistry is taught. One of the most popular of those charts first appeared 30 years ago. Now its editor, Gerhard Michal, has produced a book that summarizes metabolism (broadly defined) in graphical and textual formats. The book retains the elegance of the chart. Names of molecules are printed in a crisp, easy-to-read font, and structural formulas are shown with exemplary clarity. Color coding serves multiple purposes: to differentiate enzymes, substrates, cofactors, and effector molecules; to indicate in which group or groups of organisms a reaction has been observed; and to distinguish enzymatic reactions from regulatory effects. The primary advantage of presenting this information in book format is immediately apparent. A typical metabolic chart covers about 2 m2; the book has a total surface area nearly 10 times greater. The extra space is used to add explanatory text to the figures and to include many topics not covered by the traditional definition of metabolism. Examples include replication, transcription, translation, reaction mechanisms for proteolytic enzymes, and the role of chaperones in protein folding. Illustrating these topics is not as straightforward as delineating a metabolic pathway, but the author has done an admirable job of designing figures that clarify these and other aspects of biochemistry and complement the accompanying text. A potential deficiency of book format is the inability to clearly show links between different realms of metabolism: carbohydrate and amino acid pathways, for example. The book overcomes this problem in two ways. A diagrammatic overview of metabolism (with references to applicable sections of the book) is printed inside its front cover, and key compounds (pyruvate, for example) have a distinctive green background to provide a visual link between pathways. (The author compares this feature to the hyperlinks in an electronic document.) The book's index is comprehensive and useful. Entries for "phenylketonuria" and "sickle cell anemia", for example, lead to commendably concise summaries of these hereditary diseases (and the relevant metabolic pathway, in the former case). Looking up a specific molecule, however, is less helpful. The listing for fumarate hydratase, a citric acid cycle enzyme, directs the reader to the chapter on special bacterial metabolism but not to the section on the citric acid cycle itself. Literature references are included at the end of each section and are mainly from the 1990s, but they could be more useful. A long section on heme proteins, for example, concludes with eight citations, but their titles are not included, so it is impossible to determine what topic each one addresses. This book will be most useful to those with a good understanding of the fundamentals of biochemistry. Some of the information it presents could easily confuse less experienced readers. For example, it classifies selenocysteine as a standard amino acid in a figure but not in the accompanying text. In the diagram of anaerobic glycolysis, a double-headed arrow for the hexokinase reaction reinforces the frustratingly common student misperception that the phosphoryl group of glucose-6-phosphate can be used to phosphorylate ADP. Biochemical Pathways compiles a large amount of information in a single source. Its good index and clear, concise text and diagrams should make it a reliable way of gaining insight into many biochemical topics. With a price similar to that of most textbooks, it merits a place in the libraries of individuals and academic departments that teach biochemistry.

  8. Concordant Signaling Pathways Produced by Pesticide Exposure in Mice Correspond to Pathways Identified in Human Parkinson's Disease

    PubMed Central

    Gollamudi, Seema; Johri, Ashu; Calingasan, Noel Y.; Yang, Lichuan; Elemento, Olivier; Beal, M. Flint

    2012-01-01

    Parkinson's disease (PD) is a neurodegenerative disease in which the etiology of 90 percent of the patients is unknown. Pesticide exposure is a major risk factor for PD, and paraquat (PQ), pyridaben (PY) and maneb (MN) are amongst the most widely used pesticides. We studied mRNA expression using transcriptome sequencing (RNA-Seq) in the ventral midbrain (VMB) and striatum (STR) of PQ, PY and paraquat+maneb (MNPQ) treated mice, followed by pathway analysis. We found concordance of signaling pathways between the three pesticide models in both the VMB and STR as well as concordance in these two brain areas. The concordant signaling pathways with relevance to PD pathogenesis were e.g. axonal guidance signaling, Wnt/?-catenin signaling, as well as pathways not previously linked to PD, e.g. basal cell carcinoma, human embryonic stem cell pluripotency and role of macrophages, fibroblasts and endothelial cells in rheumatoid arthritis. Human PD pathways previously identified by expression analysis, concordant with VMB pathways identified in our study were axonal guidance signaling, Wnt/?-catenin signaling, IL-6 signaling, ephrin receptor signaling, TGF-? signaling, PPAR signaling and G-protein coupled receptor signaling. Human PD pathways concordant with the STR pathways in our study were Wnt/?-catenin signaling, axonal guidance signaling and G-protein coupled receptor signaling. Peroxisome proliferator activated receptor delta (Ppard) and G-Protein Coupled Receptors (GPCRs) were common genes in VMB and STR identified by network analysis. In conclusion, the pesticides PQ, PY and MNPQ elicit common signaling pathways in the VMB and STR in mice, which are concordant with known signaling pathways identified in human PD, suggesting that these pathways contribute to the pathogenesis of idiopathic PD. The analysis of these networks and pathways may therefore lead to improved understanding of disease pathogenesis, and potential novel therapeutic targets. PMID:22563483

  9. A cross-study gene set enrichment analysis identifies critical pathways in endometriosis

    Microsoft Academic Search

    Hongbo Zhao; Qishan Wang; Chunyan Bai; Kan He; Yuchun Pan

    2009-01-01

    BACKGROUND: Endometriosis is an enigmatic disease. Gene expression profiling of endometriosis has been used in several studies, but few studies went further to classify subtypes of endometriosis based on expression patterns and to identify possible pathways involved in endometriosis. Some of the observed pathways are more inconsistent between the studies, and these candidate pathways presumably only represent a fraction of

  10. A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text

    PubMed Central

    Miwa, Makoto; Ohta, Tomoko; Rak, Rafal; Rowley, Andrew; Kell, Douglas B.; Pyysalo, Sampo; Ananiadou, Sophia

    2013-01-01

    Motivation: To create, verify and maintain pathway models, curators must discover and assess knowledge distributed over the vast body of biological literature. Methods supporting these tasks must understand both the pathway model representations and the natural language in the literature. These methods should identify and order documents by relevance to any given pathway reaction. No existing system has addressed all aspects of this challenge. Method: We present novel methods for associating pathway model reactions with relevant publications. Our approach extracts the reactions directly from the models and then turns them into queries for three text mining-based MEDLINE literature search systems. These queries are executed, and the resulting documents are combined and ranked according to their relevance to the reactions of interest. We manually annotate document-reaction pairs with the relevance of the document to the reaction and use this annotation to study several ranking methods, using various heuristic and machine-learning approaches. Results: Our evaluation shows that the annotated document-reaction pairs can be used to create a rule-based document ranking system, and that machine learning can be used to rank documents by their relevance to pathway reactions. We find that a Support Vector Machine-based system outperforms several baselines and matches the performance of the rule-based system. The success of the query extraction and ranking methods are used to update our existing pathway search system, PathText. Availability: An online demonstration of PathText 2 and the annotated corpus are available for research purposes at http://www.nactem.ac.uk/pathtext2/. Contact: makoto.miwa@manchester.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23813008

  11. Aldehyde Dehydrogenases in Arabidopsis thaliana: Biochemical Requirements, Metabolic Pathways, and Functional Analysis

    PubMed Central

    Stiti, Naim; Missihoun, Tagnon D.; Kotchoni, Simeon O.; Kirch, Hans-Hubert; Bartels, Dorothea

    2011-01-01

    Aldehyde dehydrogenases (ALDHs) are a family of enzymes which catalyze the oxidation of reactive aldehydes to their corresponding carboxylic acids. Here we summarize molecular genetic and biochemical analyses of selected Arabidopsis ALDH genes. Aldehyde molecules are very reactive and are involved in many metabolic processes but when they accumulate in excess they become toxic. Thus activity of aldehyde dehydrogenases is important in regulating the homeostasis of aldehydes. Overexpression of some ALDH genes demonstrated an improved abiotic stress tolerance. Despite the fact that several reports are available describing a role for specific ALDHs, their precise physiological roles are often still unclear. Therefore a number of genetic and biochemical tools have been generated to address the function with an emphasis on stress-related ALDHs. ALDHs exert their functions in different cellular compartments and often in a developmental and tissue specific manner. To investigate substrate specificity, catalytic efficiencies have been determined using a range of substrates varying in carbon chain length and degree of carbon oxidation. Mutational approaches identified amino acid residues critical for coenzyme usage and enzyme activities. PMID:22639603

  12. Computationally identifying virulence factors based on KEGG pathways.

    PubMed

    Cui, Weiren; Chen, Lei; Huang, Tao; Gao, Qian; Jiang, Min; Zhang, Ning; Zheng, Lulu; Feng, Kaiyan; Cai, Yudong; Wang, Hongwei

    2013-06-01

    Virulence factors are molecules that play very important roles in enhancing the pathogen's capability in causing diseases. Many efforts were made to investigate the mechanism of virulence factors using in silico methods. In this study, we present a novel computational method to predict virulence factors by integrating protein-protein interactions in a STRING database and biological pathways in the KEGG. Three specific species were studied according to their records in the VFDB. They are Campylobacter jejuni NCTC 11168, Escherichia coli O6?:?K15?:?H31 536 (UPEC) and Pseudomonas aeruginosa PAO1. The prediction accuracies reached were 0.9467, 0.9575 and 0.9180, respectively. Metabolism pathways, flagellar assembly and chemotaxis may be of importance for virulence based on the analysis of the optimal feature sets we obtained. We hope this can provide some insight and guidance for related research. PMID:23519087

  13. Characterization of the biochemical-pathway of uranium (VI) reduction in facultative anaerobic bacteria.

    PubMed

    Mtimunye, Phalazane J; Chirwa, Evans M N

    2014-10-01

    Cultures of U(VI) reducing bacteria sourced from abandoned uranium mine tailing dam were evaluated for their ability to reduce U(VI) to U(IV). The species in the cultures reduced U(VI) in solutions with initial U(VI) concentration up to 400mgL(-)(1) under a near neutral pH of 6.5. The electron flow pathway and fate of reduced species was also analysed in the individual species in order to evaluate the potential for control and optimisation of the reduction potential at the biochemical level. The results showed that U(VI) reduction in live cells was completely blocked by the NADH-dehydrogenase inhibitor, rotenone (C23H22O6), and thioredoxin inhibitor, cadmium chloride (CdCl2), showing that U(VI) reduction involves the electron flow through NADH-dehydrogenase, a primary electron donor to the electron transport respiratory (ETR) system. Mass balance analysis of uranium species aided by visual and electron microscopy suggest that most U(VI) reduction occurred on the cell surface of the isolated species. This finding indicates the possibility of easy uranium recovery for beneficial use through biological remediation. Should the U(VI) be reduced inside the cell, recovery would require complete disruption of the cells and therefore would be difficult. The study contributes new knowledge on the underlying mechanisms in the U(VI) reduction in facultative anaerobes. PMID:25065785

  14. Biochemical Modulation of Lipid Pathway in Microalgae Dunaliella sp. for Biodiesel Production

    PubMed Central

    Talebi, Ahmad Farhad; Tohidfar, Masoud; Mousavi Derazmahalleh, Seyedeh Mahsa; Sulaiman, Alawi; Baharuddin, Azhari Samsu; Tabatabaei, Meisam

    2015-01-01

    Exploitation of renewable sources of energy such as algal biodiesel could turn energy supplies problem around. Studies on a locally isolated strain of Dunaliella sp. showed that the mean lipid content in cultures enriched by 200?mg?L?1 myoinositol was raised by around 33% (1.5 times higher than the control). Similarly, higher lipid productivity values were achieved in cultures treated by 100 and 200?mg?L?1 myoinositol. Fluorometry analyses (microplate fluorescence and flow cytometry) revealed increased oil accumulation in the Nile red-stained algal samples. Moreover, it was predicted that biodiesel produced from myoinositol-treated cells possessed improved oxidative stability, cetane number, and cloud point values. From the genomic point of view, real-time analyses revealed that myoinositol negatively influenced transcript abundance of AccD gene (one of the key genes involved in lipid production pathway) due to feedback inhibition and that its positive effect must have been exerted through other genes. The findings of the current research are not to interprete that myoinositol supplementation could answer all the challenges faced in microalgal biodiesel production but instead to show that “there is a there there” for biochemical modulation strategies, which we achieved, increased algal oil quantity and enhanced resultant biodiesel quality. PMID:26146623

  15. Receptor-Drug Interaction: Europium Employment for Studying the Biochemical Pathway of G-Protein-Coupled Receptor Activation

    PubMed Central

    Antonio, Colabufo Nicola; Grazia, Perrone Maria; Marialessandra, Contino; Francesco, Berardi; Roberto, Perrone

    2007-01-01

    In medicinal chemistry field, the biochemical pathways, involved in 7-transmembrane domains G-protein coupled receptors (GPCRs) activation, are commonly studied to establish the activity of ligands towards GPCRs. The most studied steps are the measurement of activated GTP-? subunit and stimulated intracellular cAMP. At the present, many researchers defined agonist or antagonist activity of potential GPCRs drugs employing [35S]GTP?S or [3H]cAMP as probes. Recently, the corresponding lanthanide labels Eu-GTP and Eu-cAMP as alternative to radiochemicals have been developed because they are highly sensitive, easy to automate, easily synthesized, they display a much longer shelf-life and they can be used in multilabel experiments. In the present review, the receptor-drug interaction by europium employment for studying the biochemical pathway of GPCR activation has been focused. Moreover, comparative studies between lanthanide label probes and the corresponding radiolabeled compounds have been carried out. PMID:18350113

  16. Investigations into plant biochemical wound-response pathways involved in the production of aphid-induced plant volatiles.

    PubMed

    Girling, Robbie D; Madison, Rachael; Hassall, Mark; Poppy, Guy M; Turner, John G

    2008-01-01

    Feeding damage to plants by insect herbivores induces the production of plant volatiles, which are attractive to the herbivores natural enemies. Little is understood about the plant biochemical pathways involved in aphid-induced plant volatile production. The aphid parasitoid Diaeretiella rapae can detect and respond to aphid-induced volatiles produced by Arabidopsis thaliana. When given experience of those volatiles, it can learn those cues and can therefore be used as a novel biosensor to detect them. The pathways involved in aphid-induced volatile production were investigated by comparing the responses of D. rapae to volatiles from a number of different transgenic mutants of A. thaliana, mutated in their octadecanoid, ethylene or salicylic acid wound-response pathways and also from wild-type plants. Plants were either undamaged or infested by the peach-potato aphid, Myzus persicae. It is demonstrated that the octadecanoid pathway and specifically the COI1 gene are required for aphid-induced volatile production. The presence of salicylic acid is also involved in volatile production. Using this model system, in combination with A. thaliana plants with single point gene mutations, has potential for the precise dissection of biochemical pathways involved in the production of aphid-induced volatiles. PMID:18583348

  17. Identifiability and inference of pathway motifs by epistasis analysis

    NASA Astrophysics Data System (ADS)

    Phenix, Hilary; Perkins, Theodore; Kærn, Mads

    2013-06-01

    The accuracy of genetic network inference is limited by the assumptions used to determine if one hypothetical model is better than another in explaining experimental observations. Most previous work on epistasis analysis—in which one attempts to infer pathway relationships by determining equivalences among traits following mutations—has been based on Boolean or linear models. Here, we delineate the ultimate limits of epistasis-based inference by systematically surveying all two-gene network motifs and use symbolic algebra with arbitrary regulation functions to examine trait equivalences. Our analysis divides the motifs into equivalence classes, where different genetic perturbations result in indistinguishable experimental outcomes. We demonstrate that this partitioning can reveal important information about network architecture, and show, using simulated data, that it greatly improves the accuracy of genetic network inference methods. Because of the minimal assumptions involved, equivalence partitioning has broad applicability for gene network inference.

  18. Hypericin biosynthesis in Hypericum hookerianum Wight and Arn: investigation on biochemical pathways using metabolite inhibitors and suppression subtractive hybridization.

    PubMed

    Pillai, Padmesh P; Nair, Aswati R

    2014-10-01

    The biochemical pathway to hypericin biosynthesis is presumed to be polyketide synthase (PKS) mediated, but it has not been experimentally validated, and no alternate route (chorismate/o-succinylbenzoate pathway) has been analyzed. We report here our earlier developed auxin inducible culture systems of Hypericum hookerianum as a model, to study the metabolic pathway to hypericin synthesis. Inhibitors of the alternate pathway at varying concentrations showed steady synthesis of total hypericins with means of 2.80±0.22, 18.75±0.01; 16.39±3.75, 29.60±1.90 (mevinolin) 2.53±0.10, 18.12±0.56; 0.14±0.01, 14.28±1.11 (fosmidomycin) and 2.7±0.35, 18.75±0.61; 0.14±0.01, 12.80±1.09 mg g(-1) DW (glyphosate) in the control and auxin-induced shoot and shoot-forming callus cultures, respectively. SSH analysis classified the differentially expressed sequences into protein synthesis (38%), modification (20%), electron transport (9%) and remaining as unclassified (11%) and unknown proteins (22%). Functional annotation of sequences indicates the presence of additional protein components besides PKS activity. Our results demonstrate direct biochemical and molecular evidence of PKS hypothesis of hypericin biosynthesis for the first time. PMID:25282172

  19. Identifying Drug Active Pathways from Gene Networks Estimated by Gene Expression Data

    Microsoft Academic Search

    Yoshinori Tamada; Seiya Imoto; Kousuke Tashiro; Satoru Kuhara; Satoru Miyano

    2005-01-01

    We present a computational method for identifying genes and their regulatory pathways in?u- enced by a drug, using microarray gene expression data collected by single gene disruptions and drug responses. The automatic identiflcation of such genes and pathways in organisms' cells is an important problem for pharmacogenomics and the tailor-made medication. Our method estimates regulatory relationships between genes as a

  20. Compensatory plasticity at an identified synapse tunes a visuomotor pathway.

    PubMed

    Rogers, Stephen M; Krapp, Holger G; Burrows, Malcolm; Matheson, Thomas

    2007-04-25

    We characterized homeostatic plasticity at an identified sensory-motor synapse in an insect, which maintains constant levels of motor drive as locusts transform from their solitarious phase to their gregarious swarming phase. The same mechanism produces behaviorally relevant changes in response timing that can be understood in the context of an animal's altered behavioral state. For individual animals of either phase, different looming objects elicited different spiking responses in a visual looming detector interneuron, descending contralateral movement detector (DCMD), yet its synaptic drive to a leg motoneuron, fast extensor tibiae (FETi), always had the same maximum amplitude. Gregarious locust DCMDs produced more action potentials and had higher firing frequencies, but individual postsynaptic potentials (PSPs) elicited in FETi were half the amplitude of those in solitarious locusts. A model suggested that this alone could not explain the similarity in overall amplitude, and we show that facilitation increased the maximum compound PSP amplitude in gregarious animals. There was the same linear relationship between times of peak DCMD firing before collision and the size/velocity of looming objects in both phases. The DCMD-FETi synapse transformed this relationship nonlinearly, such that peak amplitudes of compound PSPs occurred disproportionately earlier for smaller/faster objects. Furthermore, the peak PSP amplitude occurred earlier in gregarious than in solitarious locusts, indicating a differential tuning. Homeostatic modulation of the amplitude, together with a nonlinear synaptic transformation of timing, acted together to tune the DCMD-FETi system so that swarming gregarious locusts respond earlier to small moving objects, such as conspecifics, than solitarious locusts. PMID:17460075

  1. Gene expression profiling identifies emerging oncogenic pathways operating in extranodal NK/T-cell lymphoma, nasal-type

    E-print Network

    Paris-Sud XI, Université de

    1 Gene expression profiling identifies emerging oncogenic pathways operating in extranodal NK in the frequently deleted 6q21 region. This study highlights emerging oncogenic pathways in NKTCL and identifies

  2. Identifying the biological pathways underlying human focal epilepsy: from complexity to coherence to centrality.

    PubMed

    Mirza, Nasir; Appleton, Richard; Burn, Sasha; Carr, Daniel; Crooks, Daniel; du Plessis, Daniel; Duncan, Roderick; Farah, Jibril Osman; Josan, Vivek; Miyajima, Fabio; Mohanraj, Rajiv; Shukralla, Arif; Sills, Graeme J; Marson, Anthony G; Pirmohamed, Munir

    2015-08-01

    Numerous diverse biological pathways are dysregulated in the epileptic focus. Which of these pathways are most critical in producing the biological abnormalities that lead to epilepsy? Answering this question is key to identifying the primary causes of epilepsy and for discovering new therapeutic strategies with greater efficacy than currently available antiepileptics (AEDs). We have performed the largest genome-wide transcriptomic analysis to date comparing epileptic with normal human hippocampi. We have identified 118 differentially expressed and, for the first time, differentially connected pathways in the epileptic focus. Using network mapping techniques, we have shown that these dysregulated pathways, though seemingly disparate, form a coherent interconnected central network. Using closeness centrality analysis, we have identified that the most influential hub pathways in this network are signalling through G protein-coupled receptors, in particular opioid receptors, and their downstream effectors PKA/CREB and DAG/IP3. Next, we have objectively demonstrated that genetic association of gene sets in independent genome-wide association studies (GWASs) can be used to identify causally relevant gene sets: we show that proven causal epilepsy genes, which cause familial Mendelian epilepsy syndromes, are associated in published sporadic epilepsy GWAS results. Using the same technique, we have shown that central pathways identified (opioid receptor and PKA/CREB and DAG/IP3 signalling pathways) are genetically associated with focal epilepsy and, hence, likely causal. Published functional studies in animal models provide evidence of a role for these pathways in epilepsy. Our work shows that these pathways play a central role in human focal epilepsy and that they are important currently unexploited antiepileptic drug targets. PMID:25941323

  3. The Use of Functional Chemical-Protein Associations to Identify Multi-Pathway Renoprotectants

    PubMed Central

    Xu, Jia; Meng, Kexin; Zhang, Rui; Yang, He; Liao, Chang; Zhu, Wenliang; Jiao, Jundong

    2014-01-01

    Typically, most nephropathies can be categorized as complex human diseases in which the cumulative effect of multiple minor genes, combined with environmental and lifestyle factors, determines the disease phenotype. Thus, multi-target drugs would be more likely to facilitate comprehensive renoprotection than single-target agents. In this study, functional chemical-protein association analysis was performed to retrieve multi-target drugs of high pathway wideness from the STITCH 3.1 database. Pathway wideness of a drug evaluated the efficiency of regulation of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in quantity. We identified nine experimentally validated renoprotectants that exerted remarkable impact on KEGG pathways by targeting a limited number of proteins. We selected curcumin as an illustrative compound to display the advantage of multi-pathway drugs on renoprotection. We compared curcumin with hemin, an agonist of heme oxygenase-1 (HO-1), which significantly affects only one KEGG pathway, porphyrin and chlorophyll metabolism (adjusted p?=?1.5×10?5). At the same concentration (10 µM), both curcumin and hemin equivalently mitigated oxidative stress in H2O2-treated glomerular mesangial cells. The benefit of using hemin was derived from its agonistic effect on HO-1, providing relief from oxidative stress. Selective inhibition of HO-1 completely blocked the action of hemin but not that of curcumin, suggesting simultaneous multi-pathway intervention by curcumin. Curcumin also increased cellular autophagy levels, enhancing its protective effect; however, hemin had no effects. Based on the fact that the dysregulation of multiple pathways is implicated in the etiology of complex diseases, we proposed a feasible method for identifying multi-pathway drugs from compounds with validated targets. Our efforts will help identify multi-pathway agents capable of providing comprehensive protection against renal injuries. PMID:24830678

  4. Preferential Activation of the Hedgehog Pathway by Epigenetic Modulations in HPV Negative HNSCC Identified with Meta-Pathway Analysis

    PubMed Central

    Fertig, Elana J.; Markovic, Ana; Danilova, Ludmila V.; Gaykalova, Daria A.; Cope, Leslie; Chung, Christine H.; Ochs, Michael F.; Califano, Joseph A.

    2013-01-01

    Head and neck squamous cell carcinoma (HNSCC) is largely divided into two groups based on their etiology, human papillomavirus (HPV)-positive and –negative. Global DNA methylation changes are known to drive oncogene and tumor suppressor expression in primary HNSCC of both types. However, significant heterogeneity in DNA methylation within the groups results in different transcriptional profiles and clinical outcomes. We applied a meta-pathway analysis to link gene expression changes to DNA methylation in distinguishing HNSCC subtypes. This approach isolated specific epigenetic changes controlling expression in HPV? HNSCC that distinguish it from HPV+ HNSCC. Analysis of genes identified Hedgehog pathway activation specific to HPV? HNSCC. We confirmed that GLI1, the primary Hedgehog target, showed higher expression in tumors compared to normal samples with HPV? tumors having the highest GLI1 expression, suggesting that increased expression of GLI1 is a potential driver in HPV? HNSCC. Our algorithm for integration of DNA methylation and gene expression can infer biologically significant molecular pathways that may be exploited as therapeutics targets. Our results suggest that therapeutics targeting the Hedgehog pathway may be of benefit in HPV? HNSCC. Similar integrative analysis of high-throughput coupled DNA methylation and expression datasets may yield novel insights into deregulated pathways in other cancers. PMID:24223768

  5. Systems analysis utilising pathway interactions identifies sonic hedgehog pathway as a primary biomarker and oncogenic target in hepatocellular carcinoma.

    PubMed

    Efroni, Sol; Meerzaman, Daoud; Schaefer, Carl F; Greenblum, Sharon; Soo-Lyu, Myung; Hu, Ying; Cultraro, Constance; Meshorer, Eran; Buetow, Kenneth H

    2013-12-01

    The development and progression of cancer is associated with disruption of biological networks. Historically studies have identified sets of signature genes involved in events ultimately leading to the development of cancer. Identification of such sets does not indicate which biologic processes are oncogenic drivers and makes it difficult to identify key networks to target for interventions. Using a comprehensive, integrated computational approach, the authors identify the sonic hedgehog (SHH) pathway as the gene network that most significantly distinguishes tumour and tumour-adjacent samples in human hepatocellular carcinoma (HCC). The analysis reveals that the SHH pathway is commonly activated in the tumour samples and its activity most significantly differentiates tumour from the non-tumour samples. The authors experimentally validate these in silico findings in the same biologic material using Western blot analysis. This analysis reveals that the expression levels of SHH, phosphorylated cyclin B1, and CDK7 levels are much higher in most tumour tissues as compared to normal tissue. It is also shown that siRNA-mediated silencing of SHH gene expression resulted in a significant reduction of cell proliferation in a liver cancer cell line, SNU449 indicating that SHH plays a major role in promoting cell proliferation in liver cancer. The SHH pathway is a key network underpinning HCC aetiology which may guide the development of interventions for this most common form of human liver cancer. PMID:24712101

  6. Metabolic engineering of a complex biochemical pathway: The lysine and threonine biosynthesis as an example

    Microsoft Academic Search

    Eric Dewaele; Adrian Craciun; Marc Vauterin; Valerie Frankard; Emmanuel Suharyanto; Johannes Tadesse; Michel Jacobs

    2002-01-01

    The nutritional quality of crop plants is determined by their content in essential amino acids provided in food for humans or in feed for monogastric animals. Amino acid composition of crop–based diets can be improved via manipulation of the properties of key enzymes of amino acid biosynthetic pathways by mutation and transformation. We focused on the aspartate-derived amino acid pathway

  7. Hydrograph Separations can Identify Contaminant-Specific Pathways for Conservation Targeting in a Tile-Drained Watershed

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Water quality issues continue to vex agriculture. Understanding contaminant-specific pathways could help clarify effective water quality management strategies in watersheds. Hypothesis: If conducted at nested scales, hydrograph separation techniques can identify contaminant-specific pathways that co...

  8. IDENTIFYING DISEASE RESISTANCE GENES AND PATHWAYS THROUGH HOST-PATHOGEN PROTEIN INTERACTIONS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A major objective of both animal and plant genomics research is to identify disease resistance genes and pathways. Popular approaches to achieve this goal include candidate gene testing, genome-wide QTL screens, and DNA microarrays. We argue that the two-hybrid assay, which detects protein-protein...

  9. Probabilistic approach to identify sensitive parameter distributions in multimedia pathway analysis.

    SciTech Connect

    Kamboj, S.; Gnanapragasam, E.; LePoire, D.; Biwer, B. M.; Cheng, J.; Arnish, J.; Yu, C.; Chen, S. Y.; Mo, T.; Abu-Eid, R.; Thaggard, M.; Environmental Assessment; NRC

    2002-01-01

    Sensitive parameter distributions were identified with the use of probabilistic analysis in the RESRAD computer code. RESRAD is a multimedia pathway analysis code designed to evaluate radiological exposures resulting from radiological contamination in soil. The dose distribution was obtained by using a set of default parameter distribution/values. Most of the variations in the output dose distribution could be attributed to uncertainty in a small set of input parameters that could be considered as sensitive parameter distributions. The identification of the sensitive parameters is a first step in the prioritization of future research and information gathering. When site-specific parameter distribution/values are available for an actual site, the same process should be used with these site-specific data. Regression analysis used to identify sensitive parameters indicated that the dominant pathways depended on the radionuclide and source configurations. However, two parameter distributions were sensitive for many radionuclides: the external shielding factor when external exposure was the dominant pathway and the plant transfer factor when plant ingestion was the dominant pathway. No single correlation or regression coefficient can be used alone to identify sensitive parameters in all the cases. The coefficients are useful guides, but they have to be used in conjunction with other aids, such as scatter plots, and should undergo further analysis.

  10. Molecular & Biochemical Parasitology 133 (2004) 4551 Arachidonic acid synthetic pathways of the oyster protozoan parasite,

    E-print Network

    Hartley, Troy W.

    2004-01-01

    of the oyster protozoan parasite, Perkinsus marinus: evidence for usage of a delta-8 pathway Fu-Lin E. Chua Received 24 June 2003; accepted 28 August 2003 Abstract The meront stage of the oyster protozoan parasite; Oyster; Oyster parasite; Perkinsus marinus 1. Introduction Although parasitic protozoans effectively

  11. "Campylobacter upsaliensis" isolated from cats as identified by DNA relatedness and biochemical features.

    PubMed Central

    Fox, J G; Maxwell, K O; Taylor, N S; Runsick, C D; Edmonds, P; Brenner, D J

    1989-01-01

    Campylobacter spp. were isolated from the feces of 20 (58%) of 53 asymptomatic cats during routine physical examination while the cats were maintained in an accredited quarantine facility. Fifteen of these Campylobacter spp. were identified phenotypically as Campylobacter jejuni, and two were identified as C. coli. DNA-DNA hybridization (hydroxyapatite method) was used to confirm the identification of three thermotolerant catalase-negative isolates. They were 80 to 100% related to each other and to the type strain of "C. upsaliensis" in reassociation reactions under optimal conditions and a stringent hybridization criterion. These strains were 75 to 100% interrelated and less than 12% related to type strains of other Campylobacter species. These strains represent the first reported feline isolate of "C. upsaliensis" and show that cats used in biomedical research can harbor this and other Campylobacter species. PMID:2584385

  12. Alterations of the biochemical pathways of plants by the air pollutant ozone: which are the true gauges of injury?

    PubMed

    Heath, Robert L

    2007-01-01

    Plant strategies to survive ozone stress include exclusion or tolerance of ozone. If these processes fail, past observations of ozone injury have indicated many physiological and metabolic changes then occur; most of these changes are likely to have been initiated at the level of gene expression, suggesting signal transduction. In the last decade considerable understanding of the biochemical process within plants has been developed. Currently there are several hypotheses regarding a response of plants to ozone fumigation: [1] membrane dysfunction and alteration of purpose; [2] stress ethylene interactions; [3] impairment of photosynthesis via changes in Rubisco levels and the guard cells so that the stomata do not track correctly the environment; [4] antioxidant protection through metabolites and enzyme systems to reduce the oxidant load; and [5] general impairment or disruption of metabolic pathways. Many believe that free radicals and other oxidative products, formed in plant leaves under ozone exposure, are responsible for much of the spread of the biochemical alterations. There are obvious chemicals that may account for the changes that are observed, such as hydrogen peroxide. Once the ozone enters the tissue, evidence suggests the first line of defense is a range of antioxidants, such as ascorbate, glutathione peroxidase, superoxide dismutase, and catalase. If overwhelmed, subsequent events occur which are highly suggestive of systemic acquired resistance. Furthermore, other defensive indicators, such as salicylic acid and jasmonic acid, tend to increase, but more slowly than ethylene, and spread their signaling effects more widely in the plant. The primary set of metabolic reactions that ozone triggers is thought to be "wounding" responses with a secondary response of senescence. The dramatic strides in understanding the genetic make-up of plants, gene control, and signal transduction/control over the last few years will only accelerate in the future. We need now to have an understanding of those events that can be translated into more detailed schemes of how ozone alters much of the basic metabolism of plants and how plants counteract or cope with ozone. What is now known about how varied biochemicals and their pathways are changed upon ozone exposure will be discussed. PMID:17450287

  13. Combined Analysis of SNP Array Data Identifies Novel CNV Candidates and Pathways in Ependymoma and Mesothelioma

    PubMed Central

    Wajnberg, Gabriel; Carvalho, Benilton S.; Ferreira, Carlos G.; Passetti, Fabio

    2015-01-01

    Copy number variation is a class of structural genomic modifications that includes the gain and loss of a specific genomic region, which may include an entire gene. Many studies have used low-resolution techniques to identify regions that are frequently lost or amplified in cancer. Usually, researchers choose to use proprietary or non-open-source software to detect these regions because the graphical interface tends to be easier to use. In this study, we combined two different open-source packages into an innovative strategy to identify novel copy number variations and pathways associated with cancer. We used a mesothelioma and ependymoma published datasets to assess our tool. We detected previously described and novel copy number variations that are associated with cancer chemotherapy resistance. We also identified altered pathways associated with these diseases, like cell adhesion in patients with mesothelioma and negative regulation of glutamatergic synaptic transmission in ependymoma patients. In conclusion, we present a novel strategy using open-source software to identify copy number variations and altered pathways associated with cancer. PMID:26185765

  14. Identifying drug effects via pathway alterations using an integer linear programming optimization formulation on phosphoproteomic data.

    PubMed

    Mitsos, Alexander; Melas, Ioannis N; Siminelakis, Paraskeuas; Chairakaki, Aikaterini D; Saez-Rodriguez, Julio; Alexopoulos, Leonidas G

    2009-12-01

    Understanding the mechanisms of cell function and drug action is a major endeavor in the pharmaceutical industry. Drug effects are governed by the intrinsic properties of the drug (i.e., selectivity and potency) and the specific signaling transduction network of the host (i.e., normal vs. diseased cells). Here, we describe an unbiased, phosphoproteomic-based approach to identify drug effects by monitoring drug-induced topology alterations. With our proposed method, drug effects are investigated under diverse stimulations of the signaling network. Starting with a generic pathway made of logical gates, we build a cell-type specific map by constraining it to fit 13 key phopshoprotein signals under 55 experimental conditions. Fitting is performed via an Integer Linear Program (ILP) formulation and solution by standard ILP solvers; a procedure that drastically outperforms previous fitting schemes. Then, knowing the cell's topology, we monitor the same key phosphoprotein signals under the presence of drug and we re-optimize the specific map to reveal drug-induced topology alterations. To prove our case, we make a topology for the hepatocytic cell-line HepG2 and we evaluate the effects of 4 drugs: 3 selective inhibitors for the Epidermal Growth Factor Receptor (EGFR) and a non-selective drug. We confirm effects easily predictable from the drugs' main target (i.e., EGFR inhibitors blocks the EGFR pathway) but we also uncover unanticipated effects due to either drug promiscuity or the cell's specific topology. An interesting finding is that the selective EGFR inhibitor Gefitinib inhibits signaling downstream the Interleukin-1alpha (IL1alpha) pathway; an effect that cannot be extracted from binding affinity-based approaches. Our method represents an unbiased approach to identify drug effects on small to medium size pathways which is scalable to larger topologies with any type of signaling interventions (small molecules, RNAi, etc). The method can reveal drug effects on pathways, the cornerstone for identifying mechanisms of drug's efficacy. PMID:19997482

  15. Meta-Analysis of Placental Transcriptome Data Identifies a Novel Molecular Pathway Related to Preeclampsia

    PubMed Central

    van Uitert, Miranda; Moerland, Perry D.; Enquobahrie, Daniel A.; Laivuori, Hannele; van der Post, Joris A. M.; Ris-Stalpers, Carrie; Afink, Gijs B.

    2015-01-01

    Studies using the placental transcriptome to identify key molecules relevant for preeclampsia are hampered by a relatively small sample size. In addition, they use a variety of bioinformatics and statistical methods, making comparison of findings challenging. To generate a more robust preeclampsia gene expression signature, we performed a meta-analysis on the original data of 11 placenta RNA microarray experiments, representing 139 normotensive and 116 preeclamptic pregnancies. Microarray data were pre-processed and analyzed using standardized bioinformatics and statistical procedures and the effect sizes were combined using an inverse-variance random-effects model. Interactions between genes in the resulting gene expression signature were identified by pathway analysis (Ingenuity Pathway Analysis, Gene Set Enrichment Analysis, Graphite) and protein-protein associations (STRING). This approach has resulted in a comprehensive list of differentially expressed genes that led to a 388-gene meta-signature of preeclamptic placenta. Pathway analysis highlights the involvement of the previously identified hypoxia/HIF1A pathway in the establishment of the preeclamptic gene expression profile, while analysis of protein interaction networks indicates CREBBP/EP300 as a novel element central to the preeclamptic placental transcriptome. In addition, there is an apparent high incidence of preeclampsia in women carrying a child with a mutation in CREBBP/EP300 (Rubinstein-Taybi Syndrome). The 388-gene preeclampsia meta-signature offers a vital starting point for further studies into the relevance of these genes (in particular CREBBP/EP300) and their concomitant pathways as biomarkers or functional molecules in preeclampsia. This will result in a better understanding of the molecular basis of this disease and opens up the opportunity to develop rational therapies targeting the placental dysfunction causal to preeclampsia. PMID:26171964

  16. The biochemical pathway for the breakdown of methyl cyanide (acetonitrile) in bacteria.

    PubMed Central

    Firmin, J L; Gray, D O

    1976-01-01

    [2-14C]Methyl cyanide (acetonitrile) is metabolized to citrate, succinate, fumarate, malate, glutamate, pyrrolidonecarboxylic acid and aspartate. Non-radioactive acetamide and acetate compete with 14C from methyl cyanide, and [2-14C]acetate and [2-14C]methyl cyanide are metabolized at similar rates, giving identical products. This evidence, combined with the inhibitory effect of fluoroacetate and arsenite on methyl cyanide metabolism, indicates that the pathway is: methyl cyanide leads to acetamide leads to acetate leads to tricarboxylic acid-cycle intermediates. The pathway was investigated in a species of Pseudomonas (group III; N.C.I.B. 10477), but comparison of labelling patterns suggests that it also exists in several higher plants. PMID:985423

  17. Biochemical outcome of blocking the ergot alkaloid pathway of a grass endophyte.

    PubMed

    Panaccione, Daniel G; Tapper, Brian A; Lane, Geoffrey A; Davies, Elizabeth; Fraser, Karl

    2003-10-22

    Neotyphodium sp. Lp1, an endophytic fungus from perennial ryegrass (Lolium perenne), produces the mycotoxin ergovaline in infected grasses, whereas a mutant in which a particular peptide synthetase gene is knocked out does not. We examined the impact of this knockout on other constituents of the ergot alkaloid pathway. Two simple lysergic acid amides, ergine and a previously undescribed amide, were eliminated by the knockout. Lysergic acid accumulated in the knockout endophyte, but quantities were only 13% of the total lysergic acid derivatives accumulated in the wild type. Concentrations of several clavines were not substantially affected. However, a novel clavine accumulated to higher concentrations in perennial ryegrass containing the knockout strain. The results indicate that production of simple lysergic acid amides requires the activity or products of the ergovaline-associated peptide synthetase and that the regulation of ergot alkaloid production is modified in response to the relatively late block in the pathway. PMID:14558758

  18. Steady and transient fluid shear stress stimulate NO release in osteoblasts through distinct biochemical pathways

    NASA Technical Reports Server (NTRS)

    McAllister, T. N.; Frangos, J. A.

    1999-01-01

    Fluid flow has been shown to be a potent stimulus in osteoblasts and osteocytes and may therefore play an important role in load-induced bone remodeling. The objective of this study was to investigate the characteristics of flow-activated pathways. Previously we reported that fluid flow stimulates rapid and continuous release of nitric oxide (NO) in primary rat calvarial osteoblasts. Here we demonstrate that flow-induced NO release is mediated by shear stress and that this response is distinctly biphasic. Transients in shear stress associated with the onset of flow stimulated a burst in NO production (8.2 nmol/mg of protein/h), while steady flow stimulated sustained NO production (2.2 nmol/mg of protein/h). Both G-protein inhibition and calcium chelation abolished the burst phase but had no effect on sustained production. Activation of G-proteins stimulated dose-dependent NO release in static cultures of both calvarial osteoblasts and UMR-106 osteoblast-like cells. Pertussis toxin had no effect on NO release. Calcium ionophore stimulated low levels of NO production within 15 minutes but had no effect on sustained production. Taken together, these data suggest that fluid shear stress stimulates NO release by two distinct pathways: a G-protein and calcium-dependent phase sensitive to flow transients, and a G-protein and calcium-independent pathway stimulated by sustained flow.

  19. Simulated Annealing Based Algorithm for Identifying Mutated Driver Pathways in Cancer

    PubMed Central

    Li, Hai-Tao; Zhang, Yu-Lang; Zheng, Chun-Hou; Wang, Hong-Qiang

    2014-01-01

    With the development of next-generation DNA sequencing technologies, large-scale cancer genomics projects can be implemented to help researchers to identify driver genes, driver mutations, and driver pathways, which promote cancer proliferation in large numbers of cancer patients. Hence, one of the remaining challenges is to distinguish functional mutations vital for cancer development, and filter out the unfunctional and random “passenger mutations.” In this study, we introduce a modified method to solve the so-called maximum weight submatrix problem which is used to identify mutated driver pathways in cancer. The problem is based on two combinatorial properties, that is, coverage and exclusivity. Particularly, we enhance an integrative model which combines gene mutation and expression data. The experimental results on simulated data show that, compared with the other methods, our method is more efficient. Finally, we apply the proposed method on two real biological datasets. The results show that our proposed method is also applicable in real practice. PMID:24982873

  20. Method for identifying biochemical and chemical reactions and micromechanical processes using nanomechanical and electronic signal identification

    DOEpatents

    Holzrichter, John F. (Berkeley, CA); Siekhaus, Wigbert J. (Berkeley, CA)

    1997-01-01

    A scanning probe microscope, such as an atomic force microscope (AFM) or a scanning tunneling microscope (STM), is operated in a stationary mode on a site where an activity of interest occurs to measure and identify characteristic time-varying micromotions caused by biological, chemical, mechanical, electrical, optical, or physical processes. The tip and cantilever assembly of an AFM is used as a micromechanical detector of characteristic micromotions transmitted either directly by a site of interest or indirectly through the surrounding medium. Alternatively, the exponential dependence of the tunneling current on the size of the gap in the STM is used to detect micromechanical movement. The stationary mode of operation can be used to observe dynamic biological processes in real time and in a natural environment, such as polymerase processing of DNA for determining the sequence of a DNA molecule.

  1. Method for identifying biochemical and chemical reactions and micromechanical processes using nanomechanical and electronic signal identification

    DOEpatents

    Holzrichter, J.F.; Siekhaus, W.J.

    1997-04-15

    A scanning probe microscope, such as an atomic force microscope (AFM) or a scanning tunneling microscope (STM), is operated in a stationary mode on a site where an activity of interest occurs to measure and identify characteristic time-varying micromotions caused by biological, chemical, mechanical, electrical, optical, or physical processes. The tip and cantilever assembly of an AFM is used as a micromechanical detector of characteristic micromotions transmitted either directly by a site of interest or indirectly through the surrounding medium. Alternatively, the exponential dependence of the tunneling current on the size of the gap in the STM is used to detect micromechanical movement. The stationary mode of operation can be used to observe dynamic biological processes in real time and in a natural environment, such as polymerase processing of DNA for determining the sequence of a DNA molecule. 6 figs.

  2. CREB3L2-PPARg Fusion Mutation Identifies a Thyroid Signaling Pathway Regulated by Intramembrane Proteolysis

    Microsoft Academic Search

    Lingchun Zeng; Victoria Rehrmann; Seema Deshpande; Maria Tretiakova; Edwin L. Kaplan; Ingo Leibiger; Barbara Leibiger; Ulla Enberg; Catharina Larsson; Todd G. Kroll

    The discovery of gene fusion mutations, particularly in leukemia, has consistently identified new cancer pathways and led to molecular diagnostic assays and molecular-targeted chemotherapies for cancer patients. Here, we report our discovery of a novel CREB3L2-PPARg fusion mutation in thyroid carcinoma with t(3;7)(p25;q34), showing that a family of somatic PPARg fusion mutations exist in thyroid cancer. The CREB3L2-PPARg fusion encodes

  3. Genetic Screens to Identify Elements of the Decapentaplegic Signaling Pathway in Drosophila

    PubMed Central

    Raftery, L. A.; Twombly, V.; Wharton, K.; Gelbart, W. M.

    1995-01-01

    Pathways for regulation of signaling by transforming growth factor-? family members are poorly understood at present. The best genetically characterized member of this family is encoded by the Drosophila gene decapentaplegic (dpp), which is required for multiple events during fly development. We describe here the results of screens for genes required to maximize dpp signaling during embryonic dorsal-ventral patterning. Screens for genetic interactions in the zygote have identified an allele of tolloid, as well as two novel alleles of screw, a gene recently shown to encode another bone morphogenetic protein-like polypeptide. Both genes are required for patterning the dorsalmost tissues of the embryo. Screens for dpp interactions with maternally expressed genes have identified loss of function mutations in Mothers against dpp and Medea. These mutations are homozygous pupal lethal, engendering gut defects and severely reduced imaginal disks, reminiscent of dpp mutant phenotypes arising during other dpp-dependent developmental events. Genetic interaction phenotypes are consistent with reduction of dpp activity in the early embryo and in the imaginal disks. We propose that the novel screw mutations identified here titrate out some component(s) of the dpp signaling pathway. We propose that Mad and Medea encode rate-limiting components integral to dpp pathways throughout development. PMID:7705627

  4. Identifying low variance pathways for free energy calculations of molecular transformations in solution phase

    NASA Astrophysics Data System (ADS)

    Pham, Tri T.; Shirts, Michael R.

    2011-07-01

    Improving the efficiency of free energy calculations is important for many biological and materials design applications, such as protein-ligand binding affinities in drug design, partitioning between immiscible liquids, and determining molecular association in soft materials. We show that for any pair potential, moderately accurate estimation of the radial distribution function for a solute molecule is sufficient to accurately estimate the statistical variance of a sampling along a free energy pathway. This allows inexpensive analytical identification of low statistical error free energy pathways. We employ a variety of methods to estimate the radial distribution function (RDF) and find that the computationally cheap two-body "dilute gas" limit performs as well or better than 3D-RISM theory and other approximations for identifying low variance free energy pathways. With a RDF estimate in hand, we can search for pairwise interaction potentials that produce low variance. We give an example of a search minimizing statistical variance of solvation free energy over the entire parameter space of a generalized "soft core" potential. The free energy pathway arising from this optimization procedure has lower curvature in the variance and reduces the total variance by at least 50% compared to the traditional soft core solvation pathway. We also demonstrate that this optimized pathway allows free energies to be estimated with fewer intermediate states due to its low curvature. This free energy variance optimization technique is generalizable to solvation in any homogeneous fluid and for any type of pairwise potential and can be performed in minutes to hours, depending on the method used to estimate g(r).

  5. Transcriptomic and biochemical analyses identify a family of chlorhexidine efflux proteins

    PubMed Central

    Hassan, Karl A.; Jackson, Scott M.; Penesyan, Anahit; Patching, Simon G.; Tetu, Sasha G.; Eijkelkamp, Bart A.; Brown, Melissa H.; Henderson, Peter J. F.; Paulsen, Ian. T.

    2013-01-01

    Chlorhexidine is widely used as an antiseptic or disinfectant in both hospital and community settings. A number of bacterial species display resistance to this membrane-active biocide. We examined the transcriptomic response of a representative nosocomial human pathogen, Acinetobacter baumannii, to chlorhexidine to identify the primary chlorhexidine resistance elements. The most highly up-regulated genes encoded components of a major multidrug efflux system, AdeAB. The next most highly overexpressed gene under chlorhexidine stress was annotated as encoding a hypothetical protein, named here as AceI. Orthologs of the aceI gene are conserved within the genomes of a broad range of proteobacterial species. Expression of aceI or its orthologs from several other ?- or ?-proteobacterial species in Escherichia coli resulted in significant increases in resistance to chlorhexidine. Additionally, disruption of the aceI ortholog in Acinetobacter baylyi rendered it more susceptible to chlorhexidine. The AceI protein was localized to the membrane after overexpression in E. coli. This protein was purified, and binding assays demonstrated direct and specific interactions between AceI and chlorhexidine. Transport assays using [14C]-chlorhexidine determined that AceI was able to mediate the energy-dependent efflux of chlorhexidine. An E15Q AceI mutant with a mutation in a conserved acidic residue, although unable to mediate chlorhexidine resistance and transport, was still able to bind chlorhexidine. Taken together, these data are consistent with AceI being an active chlorhexidine efflux protein and the founding member of a family of bacterial drug efflux transporters. PMID:24277845

  6. Molecular and biochemical characterization of the tetralin degradation pathway in Rhodococcus sp. strain TFB

    PubMed Central

    Tomás?Gallardo, Laura; Santero, Eduardo; Camafeita, Emilio; Calvo, Enrique; Schlömann, Michael; Floriano, Belén

    2009-01-01

    Summary The tetralin biodegradation pathway in Rhodococcus sp. strain TFB, a Gram?positive bacterium resistant to genetic manipulation, was characterized using a proteomic approach. Relative protein expression in cell free extracts from tetralin? and glucose?grown cells was compared using the 2D?DIGE technique. Identification of proteins specifically expressed in tetralin?grown cells was used to characterize a complete set of genes involved in tetralin degradation by reverse genetics. We propose a tetralin degradation pathway analogous to that described for Sphingomonas macrogolitabida strain TFA. TFB thn genes are organized into three operons; two contain all of the structural genes and are transcribed in the same direction, while the third operon, thnST, is transcribed in the opposite direction and encodes a two?component regulatory system, whose transcription is higher in tetralin?grown cells. In addition to tetralin induction, TFB thn structural genes are subject to glucose repression. Primer extension assays and translational thnA1::gfp and thnS::gfp fusions were used to characterize putative promoter regions. A mutational analysis of the thnA1 promoter region allowed us to define nucleotides within the cis regulatory elements that are important for the control of thn gene expression. PMID:21261920

  7. Transcriptome and Biochemical Analyses Revealed a Detailed Proanthocyanidin Biosynthesis Pathway in Brown Cotton Fiber

    PubMed Central

    Xiao, Yue-Hua; Yan, Qian; Ding, Hui; Luo, Ming; Hou, Lei; Zhang, Mi; Yao, Dan; Liu, Hou-Sheng; Li, Xin; Zhao, Jia; Pei, Yan

    2014-01-01

    Brown cotton fiber is the major raw material for colored cotton industry. Previous studies have showed that the brown pigments in cotton fiber belong to proanthocyanidins (PAs). To clarify the details of PA biosynthesis pathway in brown cotton fiber, gene expression profiles in developing brown and white fibers were compared via digital gene expression profiling and qRT-PCR. Compared to white cotton fiber, all steps from phenylalanine to PA monomers (flavan-3-ols) were significantly up-regulated in brown fiber. Liquid chromatography mass spectrometry analyses showed that most of free flavan-3-ols in brown fiber were in 2, 3-trans form (gallocatechin and catechin), and the main units of polymeric PAs were trihydroxylated on B ring. Consistent with monomeric composition, the transcript levels of flavonoid 3?, 5?-hydroxylase and leucoanthocyanidin reductase in cotton fiber were much higher than their competing enzymes acting on the same substrates (dihydroflavonol 4-reductase and anthocyanidin synthase, respectively). Taken together, our data revealed a detailed PA biosynthesis pathway wholly activated in brown cotton fiber, and demonstrated that flavonoid 3?, 5?-hydroxylase and leucoanthocyanidin reductase represented the primary flow of PA biosynthesis in cotton fiber. PMID:24466041

  8. Physiological and biochemical characteristics of adrenergic receptors and pathways in brown adipocytes

    NASA Technical Reports Server (NTRS)

    Horwitz, B. A.

    1975-01-01

    Mechanisms involved in the thermogenic response of brown adipose tissue (BAT) to sympathetic nervous stimulation (e.g., by cold exposure) and to norepinephrine (NE) release are investigated. Three effects appear to play a role in the increased oxygen consumption (and heat production) of the adipocytes: increased membrane permeability, activation of the beta-adrenergic pathway, and enhancement of Na(+)/K(+) membrane pump activity. Increased passive influx of Na(+) and efflux of K(+) due to greater permeability raise the energy demands of the Na/K pump; the pump is also stimulated by increased cyclic AMP synthesis resulting from activation by NE of membrane-bound adenyl cyclase. Studies with inhibitors such as propanolol, phentolamine, and ouabain support this hypothesis.

  9. A new screening pathway for identifying asymptomatic patients using dental panoramic radiographs

    NASA Astrophysics Data System (ADS)

    Hayashi, Tatsuro; Matsumoto, Takuya; Sawagashira, Tsuyoshi; Tagami, Motoki; Katsumata, Akitoshi; Hayashi, Yoshinori; Muramatsu, Chisako; Zhou, Xiangrong; Iida, Yukihiro; Matsuoka, Masato; Katagi, Kiyoji; Fujita, Hiroshi

    2012-03-01

    To identify asymptomatic patients is the challenging task and the essential first step in diagnosis. Findings of dental panoramic radiographs include not only dental conditions but also radiographic signs that are suggestive of possible systemic diseases such as osteoporosis, arteriosclerosis, and maxillary sinusitis. Detection of such signs on panoramic radiographs has a potential to provide supplemental benefits for patients. However, it is not easy for general dental practitioners to pay careful attention to such signs. We addressed the development of a computer-aided detection (CAD) system that detects radiographic signs of pathology on panoramic images, and the design of the framework of new screening pathway by cooperation of dentists and our CAD system. The performance evaluation of our CAD system showed the sensitivity and specificity in the identification of osteoporotic patients were 92.6 % and 100 %, respectively, and those of the maxillary sinus abnormality were 89.6 % and 73.6 %, respectively. The detection rate of carotid artery calcifications that suggests the need for further medical evaluation was approximately 93.6 % with 4.4 false-positives per image. To validate the utility of the new screening pathway, preliminary clinical trials by using our CAD system were conducted. To date, 223 panoramic images were processed and 4 asymptomatic patients with suspected osteoporosis, 7 asymptomatic patients with suspected calcifications, and 40 asymptomatic patients with suspected maxillary sinusitis were detected in our initial trial. It was suggested that our new screening pathway could be useful to identify asymptomatic patients with systemic diseases.

  10. A cellular genetics approach identifies gene-drug interactions and pinpoints drug toxicity pathway nodes.

    PubMed

    Suzuki, Oscar T; Frick, Amber; Parks, Bethany B; Trask, O Joseph; Butz, Natasha; Steffy, Brian; Chan, Emmanuel; Scoville, David K; Healy, Eric; Benton, Cristina; McQuaid, Patricia E; Thomas, Russell S; Wiltshire, Tim

    2014-01-01

    New approaches to toxicity testing have incorporated high-throughput screening across a broad-range of in vitro assays to identify potential key events in response to chemical or drug treatment. To date, these approaches have primarily utilized repurposed drug discovery assays. In this study, we describe an approach that combines in vitro screening with genetic approaches for the experimental identification of genes and pathways involved in chemical or drug toxicity. Primary embryonic fibroblasts isolated from 32 genetically-characterized inbred mouse strains were treated in concentration-response format with 65 compounds, including pharmaceutical drugs, environmental chemicals, and compounds with known modes-of-action. Integrated cellular responses were measured at 24 and 72 h using high-content imaging and included cell loss, membrane permeability, mitochondrial function, and apoptosis. Genetic association analysis of cross-strain differences in the cellular responses resulted in a collection of candidate loci potentially underlying the variable strain response to each chemical. As a demonstration of the approach, one candidate gene involved in rotenone sensitivity, Cybb, was experimentally validated in vitro and in vivo. Pathway analysis on the combined list of candidate loci across all chemicals identified a number of over-connected nodes that may serve as core regulatory points in toxicity pathways. PMID:25221565

  11. A gene signature identified using a mouse model of androgen receptor-dependent prostate cancer predicts biochemical relapse in human disease.

    PubMed

    Thompson, Vanessa C; Day, Tanya K; Bianco-Miotto, Tina; Selth, Luke A; Han, Guangzhou; Thomas, Mervyn; Buchanan, Grant; Scher, Howard I; Nelson, Colleen C; Greenberg, Norman M; Butler, Lisa M; Tilley, Wayne D

    2012-08-01

    Mutations in the androgen receptor (AR) have been detected in experimental and clinical prostate tumors. Mice with enforced prostate-specific expression of one such receptor variant, AR-E231G, invariably develop prostatic intraepithelial neoplasia by 12 weeks and metastatic prostate cancer by 52 weeks. The aim of this study was to identify genes with altered expression in the prostates of AR-E231G mice at an early stage of disease that may act as drivers of AR-mediated tumorigenesis. The gene expression profile of AR-E231G prostate tissue from 12-week-old mice was compared to an equivalent profile from mice expressing the AR-T857A receptor variant (analogous to the AR-T877A variant in LNCaP cells), which do not develop prostate tumors. One hundred and thirty-two genes were differentially expressed in AR-E231G prostates. Classification of these genes revealed enrichment for cellular pathways known to be involved in prostate cancer, including cell cycle and lipid metabolism. Suppression of two genes upregulated in the AR-E231G model, ADM and CITED1, increased cell death and reduced proliferation of human prostate cancer cells. Many genes differentially expressed in AR-E231G prostates are also deregulated in human tumors. Three of these genes, ID4, NR2F1 and PTGDS, which were expressed at consistently lower levels in clinical prostate cancer compared to nonmalignant tissues, formed a signature that predicted biochemical relapse (hazard ratio 2.2, p = 0.038). We believe that our findings support the value of this novel mouse model of prostate cancer to identify candidate therapeutic targets and/or biomarkers of human disease. PMID:22275114

  12. Metabolic profiling of chickpea-Fusarium interaction identifies differential modulation of disease resistance pathways.

    PubMed

    Kumar, Yashwant; Dholakia, Bhushan B; Panigrahi, Priyabrata; Kadoo, Narendra Y; Giri, Ashok P; Gupta, Vidya S

    2015-08-01

    Chickpea is the third most widely grown legume in the world and mainly used as a vegetarian source of human dietary protein. Fusarium wilt, caused by Fusarium oxysporum f. sp. ciceri (Foc), is one of the major threats to global chickpea production. Host resistance is the best way to protect crops from diseases; however, in spite of using various approaches, the mechanism of Foc resistance in chickpea remains largely obscure. In the present study, non-targeted metabolic profiling at several time points of resistant and susceptible chickpea cultivars using high-resolution liquid chromatography-mass spectrometry was applied to better understand the mechanistic basis of wilt resistance or susceptibility. Multivariate analysis of the data (OPLS-DA) revealed discriminating metabolites in chickpea root tissue after Foc inoculation such as flavonoids, isoflavonoids, alkaloids, amino acids and sugars. Foc inoculated resistant plants had more flavonoids and isoflavonoids along with their malonyl conjugates. Many antifungal metabolites that were induced after Foc infection viz., aurantion-obstine ?-glucosides and querecitin were elevated in resistant cultivar. Overall, diverse genetic and biochemical mechanisms were operational in the resistant cultivar for Foc defense as compared to the susceptible plant. The resistant chickpea plants employed the above-mentioned metabolic pathways as potential defense strategy against Foc. PMID:25935544

  13. Carbon and chlorine isotope analysis to identify abiotic degradation pathways of 1,1,1-trichloroethane.

    PubMed

    Palau, Jordi; Shouakar-Stash, Orfan; Hunkeler, Daniel

    2014-12-16

    This study investigates dual C-Cl isotope fractionation during 1,1,1-TCA transformation by heat-activated persulfate (PS), hydrolysis/dehydrohalogenation (HY/DH) and Fe(0). Compound-specific chlorine isotope analysis of 1,1,1-TCA was performed for the first time, and transformation-associated isotope fractionation ? bulk C and ? bulk Cl values were -4.0 ± 0.2‰ and no chlorine isotope fractionation with PS, -1.6 ± 0.2‰ and -4.7 ± 0.1‰ for HY/DH, -7.8 ± 0.4‰ and -5.2 ± 0.2‰ with Fe(0). Distinctly different dual isotope slopes (??13C/??37Cl): ? with PS, 0.33 ± 0.04 for HY/DH and 1.5 ± 0.1 with Fe(0) highlight the potential of this approach to identify abiotic degradation pathways of 1,1,1-TCA in the field. The trend observed with PS agreed with a C-H bond oxidation mechanism in the first reaction step. For HY/DH and Fe(0) pathways, different slopes were obtained although both pathways involve cleavage of a C-Cl bond in their initial reaction step. In contrast to the expected larger primary carbon isotope effects relative to chlorine for C-Cl bond cleavage, ? bulk C < ? bulk Cl was observed for HY/DH and in a similar range for reduction by Fe(0), suggesting the contribution of secondary chlorine isotope effects. Therefore, different magnitude of secondary chlorine isotope effects could at least be partly responsible for the distinct slopes between HY/DH and Fe(0) pathways. Following this dual isotope approach, abiotic transformation processes can unambiguously be identified and quantified. PMID:25379605

  14. Chemical screen identifies FDA-approved drugs and target pathways that induce precocious pancreatic endocrine differentiation

    PubMed Central

    Rovira, Meritxell; Huang, Wei; Yusuff, Shamila; Shim, Joong Sup; Ferrante, Anthony A.; Liu, Jun O.; Parsons, Michael J.

    2011-01-01

    Pancreatic ?-cells are an essential source of insulin and their destruction because of autoimmunity causes type I diabetes. We conducted a chemical screen to identify compounds that would induce the differentiation of insulin-producing ?-cells in vivo. To do this screen, we brought together the use of transgenic zebrafish as a model of ?-cell differentiation, a unique multiwell plate that allows easy visualization of lateral views of swimming larval fish and a library of clinical drugs. We identified six hits that can induce precocious differentiation of secondary islets in larval zebrafish. Three of these six hits were known drugs with a considerable background of published data on mechanism of action. Using pharmacological approaches, we have identified and characterized two unique pathways in ?-cell differentiation in the zebrafish, including down-regulation of GTP production and retinoic acid biosynthesis. PMID:22084084

  15. Riboswitches Control Fundamental Biochemical Pathways in Bacillus subtilis and Other Bacteria

    Microsoft Academic Search

    Maumita Mandal; Benjamin Boese; Jeffrey E. Barrick; Wade C. Winkler; Ronald R. Breaker

    2003-01-01

    Riboswitches are metabolite binding domains within certain messenger RNAs that serve as precision sensors for their corresponding targets. Allosteric rearrangement of mRNA structure is mediated by ligand binding, and this results in modulation of gene expression. We have identified a class of riboswitches that selectively recognizes guanine and becomes saturated at concentrations as low as 5 nM. In Bacillus subtilis,

  16. Transcriptional profiling of GBM invasion genes identifies effective inhibitors of the LIM kinase-Cofilin pathway.

    PubMed

    Park, Jun-Bum; Agnihotri, Sameer; Golbourn, Brian; Bertrand, Kelsey C; Luck, Amanda; Sabha, Nesrin; Smith, Christian A; Byron, Sara; Zadeh, Gelareh; Croul, Sidney; Berens, Michael; Rutka, James T

    2014-10-15

    Malignant gliomas are highly proliferative and invasive neoplasms where total surgical resection is often impossible and effective local radiation therapy difficult. Consequently, there is a need to develop a greater understanding of the molecular events driving invasion and to identify novel treatment targets. Using microarray analysis comparing normal brain samples and mesenchymal glioblastoma multiforme (GBM), we identified over 140 significant genes involved in cell migration and invasion. The cofilin (CFL) pathway, which disassembles actin filaments, was highly up-regulated compared to normal brain. Up-regulation of LIM domain kinase 1 and 2 (LIMK1/2), that phosphorylates and inactivates cofilin, was confirmed in an additional independent data set comparing normal brain to GBM. We identified and utilized two small molecule inhibitors BMS-5 and Cucurbitacin I directed against the cofilin regulating kinases, LIMK1 and LIMK2, to target this pathway. Significant decreases in cell viability were observed in glioma cells treated with BMS-5 and Cucurbitacin I, while no cytotoxic effects were seen in normal astrocytes that lack LIMK. BMS-5 and Cucurbitacin I promoted increased adhesion in GBM cells, and decreased migration and invasion. Collectively, these data suggest that use of LIMK inhibitors may provide a novel way to target the invasive machinery in GBM. PMID:25237832

  17. Gene expression signatures identify novel regulatory pathways during murine lung development: implications for lung tumorigenesis

    PubMed Central

    Bonner, A; Lemon, W; You, M

    2003-01-01

    Oligonucleotide array based analysis was conducted to examine the temporal pattern of gene expression across the various stages of lung development to identify regulatory pathways at key developmental time points. Whole embryo total RNA or embryonic lung total RNA was harvested from A/J mice at seven developmental stages. To investigate changes in gene expression during lung development, four samples from each stage were examined using Affymetrix U74Av2 murine oligonucleotide microarrays. From the over 12 000 genes and ESTs represented on the array, 1346 genes and ESTs were identified as having a significant change in expression between at least one time point and the others (p<0.001, Kruskal-Wallis test). Within this group of ?1300 genes, four patterns of expression were seen: (1) upregulation during the embryonic period of development (up-down); (2) upregulation during the postnatal period of lung development (down-up) and (3) fluctuating expression, up initially, down for one or more time points, and then up again (up-down-up); and (4) vice versa (down-up-down). Expression patterns of genes previously reported to be involved in pulmonary development were also examined. Using the pathway visualisation tool, GenMapp, at least three regulatory pathways were found to contain clusters of differentially expressed genes: Wnt signalling, cell cycle, and apoptosis. Furthermore, we have shown that many of the genes involved in lung development are either known oncogenes or tumour suppressor genes altered in lung cancer, such as Cyr61, Rassf1a, and Dutt1/Robo1, or putative lung cancer genes. In addition, the genes identified pertinent to early development may also serve as candidate susceptibility genes for various inherited lung cancer disorders as well as for various heritable disorders of lung development. These results will contribute to our understanding of novel aspects of the regulatory machinery for embryonic lung development and of the genes involved in lung tumorigenesis. PMID:12807961

  18. Global biochemical profiling identifies ?-hydroxypyruvate as a potential mediator of type 2 diabetes in mice and humans.

    PubMed

    Zhang, Sheng; Wang, Songyan; Puhl, Matthew D; Jiang, Xuntian; Hyrc, Krzysztof L; Laciny, Erin; Wallendorf, Michael J; Pappan, Kirk L; Coyle, Joseph T; Wice, Burton M

    2015-04-01

    Glucose-dependent insulinotropic polypeptide (GIP) and GLP-1 are incretins secreted by respective K and L enteroendocrine cells after eating and amplify glucose-stimulated insulin secretion (GSIS). This amplification has been termed the "incretin response." To determine the role(s) of K cells for the incretin response and type 2 diabetes mellitus (T2DM), diphtheria toxin-expressing (DT) mice that specifically lack GIP-producing cells were backcrossed five to eight times onto the diabetogenic NONcNZO10/Ltj background. As in humans with T2DM, DT mice lacked an incretin response, although GLP-1 release was maintained. With high-fat (HF) feeding, DT mice remained lean but developed T2DM, whereas wild-type mice developed obesity but not diabetes. Metabolomics identified biochemicals reflecting impaired glucose handling, insulin resistance, and diabetes complications in prediabetic DT/HF mice. ?-Hydroxypyruvate and benzoate levels were increased and decreased, respectively, suggesting ?-hydroxypyruvate production from d-serine. In vitro, ?-hydroxypyruvate altered excitatory properties of myenteric neurons and reduced islet insulin content but not GSIS. ?-Hydroxypyruvate-to-d-serine ratios were lower in humans with impaired glucose tolerance compared with normal glucose tolerance and T2DM. Earlier human studies unmasked a neural relay that amplifies GIP-mediated insulin secretion in a pattern reciprocal to ?-hydroxypyruvate-to-d-serine ratios in all groups. Thus, K cells may maintain long-term function of neurons and ?-cells by regulating ?-hydroxypyruvate levels. PMID:25368100

  19. Molecular and biochemical characterization of two P450 enzymes in the ecdysteroidogenic pathway of Drosophila melanogaster.

    PubMed

    Warren, James T; Petryk, Anna; Marques, Guillermo; Jarcho, Michael; Parvy, Jean-Philippe; Dauphin-Villemant, Chantal; O'Connor, Michael B; Gilbert, Lawrence I

    2002-08-20

    Five different enzymatic activities, catalyzed by both microsomal and mitochondrial cytochrome P450 monooxygenases (CYPs), are strongly implicated in the biosynthesis of ecdysone (E) from cholesterol. However, none of these enzymes have been characterized completely. The present data show that the wild-type genes of two members of the Halloween family of embryonic lethals, disembodied (dib) and shadow (sad), code for mitochondrial cytochromes P450 that mediate the last two hydroxylation reactions in the ecdysteroidogenic pathway in Drosophila, namely the C22- and C2-hydroxylases. When sad (CYP315A1) is transfected into Drosophila S2 cells, the cells metabolize 2-deoxyecdysone (2dE) to E and the [3H]ketotriol (2,22-dideoxyecdysone) to 22-deoxyecdysone. In contrast, dib (CYP302A1) is responsible for the conversion of the [3H]ketotriol to [3H]2dE. When cells are transfected with both dib and sad, they metabolize the [3H]ketotriol to [3H]E in high yield. The expression of sad and dib is concentrated within the individual segments of the developing epidermis when there is a surge of ecdysteroid midway through embryogenesis. This result occurs before the ring gland has developed and suggests that the embryonic epidermis is a site of ecdysteroid biosynthesis. This pattern then diminishes, and, during late embryogenesis, expression of both genes is concentrated in the prothoracic gland cells of the developing ring gland. Expression of dib and sad continues to be localized in this endocrine compartment during larval development, being maximal in both the late second and third instar larvae, about the time of the premolt peaks in the ecdysteroid titer. PMID:12177427

  20. Anthropogenic Molecular Markers: Tools to Identify the Sources and Transport Pathways of Pollutants

    USGS Publications Warehouse

    Takada, H.; Satoh, F.; Bothner, Michael H.; Tripp, B.W.; Johnson, C.G.; Farrington, J.W.

    1997-01-01

    The activities of modern civilization have released to the oceans a wide variety of both mobilized natural compounds and synthetic compounds not found prior to modern times. Many of these compounds provide a means of identifying sources of inputs and pathways of movement of chemicals through oceanic ecosystems and serve as molecular markers of human activities. A coastal ocean (Tokyo Bay) and a deep ocean (Deep Water Dump Site 106 in the Western North Atlantic Ocean) example are presented. In the deep ocean study, the correlation between potential sewage marker, i.e. linear alkylbenzenes (LABs), and polychlorinated biphenyls (PCBs) concentrations indicates a contribution of sewage sludge PCBs to the dump site sediments.

  1. Functional Genomic Analyses Identify Pathways Dysregulated by Progranulin Deficiency Implicating Wnt Signaling

    PubMed Central

    Rosen, Ezra Y.; Wexler, Eric M.; Versano, Revital; Coppola, Giovanni; Gao, Fuying; Winden, Kellen D.; Oldham, Michael C.; Martens, Lauren Herl; Zhou, Ping; Farese, Robert V.; Geschwind, Daniel H.

    2011-01-01

    Summary Progranulin (GRN) mutations cause frontotemporal dementia (FTD), but GRN’s function in the CNS remains largely unknown. To identify the pathways downstream of GRN, we used weighted gene co-expression network analysis (WGCNA) to develop a systems-level view of transcriptional alterations in a human neural progenitor model of GRN-deficiency. This highlighted key pathways such as apoptosis and ubiquitination in GRN deficient human neurons, while revealing an unexpected major role for the Wnt signaling pathway, which was confirmed by analysis of gene expression data from postmortem FTD brain. Furthermore, we observed that the Wnt receptor Fzd2 was one of only a few genes up-regulated at 6 weeks in a GRN knockout mouse, and that FZD2 reduction caused increased apoptosis, while its upregulation promoted neuronal survival in vitro. Together, these in vitro and in vivo data point to an adaptive role for altered Wnt signaling in GRN deficiency-mediated FTD, representing a potential therapeutic target. PMID:21943601

  2. Gene Expression Profiling Identifies Molecular Pathways Associated with Collagen VI Deficiency and Provides Novel Therapeutic Targets

    PubMed Central

    Paco, Sonia; Kalko, Susana G.; Jou, Cristina; Rodríguez, María A.; Corbera, Joan; Muntoni, Francesco; Feng, Lucy; Rivas, Eloy; Torner, Ferran; Gualandi, Francesca; Gomez-Foix, Anna M.; Ferrer, Anna; Ortez, Carlos; Nascimento, Andrés; Colomer, Jaume; Jimenez-Mallebrera, Cecilia

    2013-01-01

    Ullrich congenital muscular dystrophy (UCMD), caused by collagen VI deficiency, is a common congenital muscular dystrophy. At present, the role of collagen VI in muscle and the mechanism of disease are not fully understood. To address this we have applied microarrays to analyse the transcriptome of UCMD muscle and compare it to healthy muscle and other muscular dystrophies. We identified 389 genes which are differentially regulated in UCMD relative to controls. In addition, there were 718 genes differentially expressed between UCMD and dystrophin deficient muscle. In contrast, only 29 genes were altered relative to other congenital muscular dystrophies. Changes in gene expression were confirmed by real-time PCR. The set of regulated genes was analysed by Gene Ontology, KEGG pathways and Ingenuity Pathway analysis to reveal the molecular functions and gene networks associated with collagen VI defects. The most significantly regulated pathways were those involved in muscle regeneration, extracellular matrix remodelling and inflammation. We characterised the immune response in UCMD biopsies as being mainly mediated via M2 macrophages and the complement pathway indicating that anti-inflammatory treatment may be beneficial to UCMD as for other dystrophies. We studied the immunolocalisation of ECM components and found that biglycan, a collagen VI interacting proteoglycan, was reduced in the basal lamina of UCMD patients. We propose that biglycan reduction is secondary to collagen VI loss and that it may be contributing towards UCMD pathophysiology. Consequently, strategies aimed at over-expressing biglycan and restore the link between the muscle cell surface and the extracellular matrix should be considered. PMID:24223098

  3. An Approach for Identifying Brainstem Dopaminergic Pathways Using Resting State Functional MRI

    PubMed Central

    Vytlacil, Jason; Kayser, Andrew; Miyakawa, Asako; D’Esposito, Mark

    2014-01-01

    Here, we present an approach for identifying brainstem dopaminergic pathways using resting state functional MRI. In a group of healthy individuals, we searched for significant functional connectivity between dopamine-rich midbrain areas (substantia nigra; ventral tegmental area) and a striatal region (caudate) that was modulated by both a pharmacological challenge (the administration of the dopaminergic agonist bromocriptine) and a dopamine-sensitive cognitive trait (an individual’s working memory capacity). A significant inverted-U shaped connectivity pattern was found in a subset of midbrain-striatal connections, demonstrating that resting state fMRI data is sufficiently powerful to identify brainstem neuromodulatory brain networks. PMID:24498023

  4. Comprehensive profiling analysis of actively resorbing osteoclasts identifies critical signaling pathways regulated by bone substrate

    PubMed Central

    Purdue, P. Edward; Crotti, Tania N.; Shen, Zhenxin; Swantek, Jennifer; Li, Jun; Hill, Jonathan; Hanidu, Adedayo; Dimock, Janice; Nabozny, Gerald; Goldring, Steven R.; McHugh, Kevin P.

    2014-01-01

    As the only cells capable of efficiently resorbing bone, osteoclasts are central mediators of both normal bone remodeling and pathologies associates with excessive bone resorption. However, despite the clear evidence of interplay between osteoclasts and the bone surface in vivo, the role of the bone substrate in regulating osteoclast differentiation and activation at a molecular level has not been fully defined. Here, we present the first comprehensive expression profiles of osteoclasts differentiated on authentic resorbable bone substrates. This analysis has identified numerous critical pathways coordinately regulated by osteoclastogenic cytokines and bone substrate, including the transition from proliferation to differentiation, and sphingosine-1-phosphate signaling. Whilst, as expected, much of this program is dependent upon integrin beta 3, the pre-eminent mediator of osteoclast-bone interaction, a surprisingly significant portion of the bone substrate regulated expression signature is independent of this receptor. Together, these findings identify an important hitherto underappreciated role for bone substrate in osteoclastogenesis. PMID:25534583

  5. Integrated Genomics Identifies Convergence of Ankylosing Spondylitis with Global Immune Mediated Disease Pathways

    PubMed Central

    Uddin, Mohammed; Codner, Dianne; Mahmud Hasan, S M; Scherer, Stephen W; O’Rielly, Darren D; Rahman, Proton

    2015-01-01

    Ankylosing spondylitis(AS), a highly heritable complex inflammatory arthritis. Although, a handful of non-HLA risk loci have been identified, capturing the unexplained genetic contribution to AS pathogenesis remains a challenge attributed to additive, pleiotropic and epistatic-interactions at the molecular level. Here, we developed multiple integrated genomic approaches to quantify molecular convergence of non-HLA loci with global immune mediated diseases. We show that non-HLA genes are significantly sensitive to deleterious mutation accumulation in the general population compared with tolerant genes. Human developmental proteomics (prenatal to adult) analysis revealed that proteins encoded by non-HLA AS risk loci are 2-fold more expressed in adult hematopoietic cells.Enrichment analysis revealed AS risk genes overlap with a significant number of immune related pathways (p?pathways with other immune mediated diseases. This information will be pivotal to fully explain AS pathogenesis and identify new therapeutic targets. PMID:25980808

  6. Integrated genomics identifies convergence of ankylosing spondylitis with global immune mediated disease pathways.

    PubMed

    Uddin, Mohammed; Codner, Dianne; Mahmud Hasan, S M; Scherer, Stephen W; O'Rielly, Darren D; Rahman, Proton

    2015-01-01

    Ankylosing spondylitis(AS), a highly heritable complex inflammatory arthritis. Although, a handful of non-HLA risk loci have been identified, capturing the unexplained genetic contribution to AS pathogenesis remains a challenge attributed to additive, pleiotropic and epistatic-interactions at the molecular level. Here, we developed multiple integrated genomic approaches to quantify molecular convergence of non-HLA loci with global immune mediated diseases. We show that non-HLA genes are significantly sensitive to deleterious mutation accumulation in the general population compared with tolerant genes. Human developmental proteomics (prenatal to adult) analysis revealed that proteins encoded by non-HLA AS risk loci are 2-fold more expressed in adult hematopoietic cells.Enrichment analysis revealed AS risk genes overlap with a significant number of immune related pathways (p?pathways with other immune mediated diseases. This information will be pivotal to fully explain AS pathogenesis and identify new therapeutic targets. PMID:25980808

  7. Subnetwork-based analysis of chronic lymphocytic leukemia identifies pathways that associate with disease progression

    PubMed Central

    Chuang, Han-Yu; Rassenti, Laura; Salcedo, Michelle; Licon, Kate; Kohlmann, Alexander; Haferlach, Torsten; Foà, Robin

    2012-01-01

    The clinical course of patients with chronic lymphocytic leukemia (CLL) is heterogeneous. Several prognostic factors have been identified that can stratify patients into groups that differ in their relative tendency for disease progression and/or survival. Here, we pursued a subnetwork-based analysis of gene expression profiles to discriminate between groups of patients with disparate risks for CLL progression. From an initial cohort of 130 patients, we identified 38 prognostic subnetworks that could predict the relative risk for disease progression requiring therapy from the time of sample collection, more accurately than established markers. The prognostic power of these subnetworks then was validated on 2 other cohorts of patients. We noted reduced divergence in gene expression between leukemia cells of CLL patients classified at diagnosis with aggressive versus indolent disease over time. The predictive subnetworks vary in levels of expression over time but exhibit increased similarity at later time points before therapy, suggesting that degenerate pathways apparently converge into common pathways that are associated with disease progression. As such, these results have implications for understanding cancer evolution and for the development of novel treatment strategies for patients with CLL. PMID:22837534

  8. Subnetwork-based analysis of chronic lymphocytic leukemia identifies pathways that associate with disease progression.

    PubMed

    Chuang, Han-Yu; Rassenti, Laura; Salcedo, Michelle; Licon, Kate; Kohlmann, Alexander; Haferlach, Torsten; Foà, Robin; Ideker, Trey; Kipps, Thomas J

    2012-09-27

    The clinical course of patients with chronic lymphocytic leukemia (CLL) is heterogeneous. Several prognostic factors have been identified that can stratify patients into groups that differ in their relative tendency for disease progression and/or survival. Here, we pursued a subnetwork-based analysis of gene expression profiles to discriminate between groups of patients with disparate risks for CLL progression. From an initial cohort of 130 patients, we identified 38 prognostic subnetworks that could predict the relative risk for disease progression requiring therapy from the time of sample collection, more accurately than established markers. The prognostic power of these subnetworks then was validated on 2 other cohorts of patients. We noted reduced divergence in gene expression between leukemia cells of CLL patients classified at diagnosis with aggressive versus indolent disease over time. The predictive subnetworks vary in levels of expression over time but exhibit increased similarity at later time points before therapy, suggesting that degenerate pathways apparently converge into common pathways that are associated with disease progression. As such, these results have implications for understanding cancer evolution and for the development of novel treatment strategies for patients with CLL. PMID:22837534

  9. Correlation between biochemical findings, structural and enzymatic abnormalities in mutated HMBS identified in six Israeli families with acute intermittent porphyria.

    PubMed

    Ulbrichova, Dana; Schneider-Yin, Xiaoye; Mamet, Rivka; Saudek, Vladimir; Martasek, Pavel; Minder, Elisabeth I; Schoenfeld, Nili

    2009-01-01

    Mutations in the hydroxymethylbilane synthase (HMBS) gene are responsible for the inherited disorder of acute intermittent porphyria (AIP). AIP is diagnosed on the basis of characteristic clinical symptoms, elevated levels of urinary porphyrin precursors aminolevulinic acid (ALA) and porphobilinogen (PBG) and a decreased erythrocytic HMBS activity, although an identifiable HMBS mutation provides the ultimate proof for AIP. Six Israeli AIP families underwent biochemical and mutation analysis in order to establish an AIP diagnosis. Variability with respect to the ALA/PBG levels and HBMS activity was found among the index patients. Indeed, each family carried a unique mutation in the HMBS gene. A novel missense c.95G>C (p.R32P) was shown to be a de novo mutation in one family, along with five known mutations p.T59I, p.D178N, p.V215M, c.730_731delCT and c.982_983delCA identified in the rest of the families. Both R32P and D178N were expressed in a prokaryotic system. Recombinant p.R32P was enzymatically inactive as demonstrated by a <1% residual activity, whereas p.D178N possessed 81% of the activity of the wild type enzyme. However, the p.D178N mutant did display a shift in optimal pH and was thermo labile compared to the wild type. Among the four missense mutations, p.R32P and p.V215M had not only harmful effects on the enzyme in vitro but also were associated with high levels of ALA/PBG in patients. On the other hand, the in vitro effect of both p.T59I and p.D178N, and the impact of these mutations on the enzyme structure and function as interpreted by the 3-D structure of the Escherichia coli enzyme, were weaker than that of p.R32P and p.V215M. Concomitantly, patients carrying the p.T59I or p.D178N had normal or borderline increases in ALA/PBG concentrations although they presented characteristic clinical symptoms. These findings provided further insights into the causal relationship between HMBS mutations and AIP. PMID:19138865

  10. Integrated Analysis of Mutation Data from Various Sources Identifies Key Genes and Signaling Pathways in Hepatocellular Carcinoma

    PubMed Central

    Wei, Lin; Tang, Ruqi; Lian, Baofeng; Zhao, Yingjun; He, Xianghuo; Xie, Lu

    2014-01-01

    Background Recently, a number of studies have performed genome or exome sequencing of hepatocellular carcinoma (HCC) and identified hundreds or even thousands of mutations in protein-coding genes. However, these studies have only focused on a limited number of candidate genes, and many important mutation resources remain to be explored. Principal Findings In this study, we integrated mutation data obtained from various sources and performed pathway and network analysis. We identified 113 pathways that were significantly mutated in HCC samples and found that the mutated genes included in these pathways contained high percentages of known cancer genes, and damaging genes and also demonstrated high conservation scores, indicating their important roles in liver tumorigenesis. Five classes of pathways that were mutated most frequently included (a) proliferation and apoptosis related pathways, (b) tumor microenvironment related pathways, (c) neural signaling related pathways, (d) metabolic related pathways, and (e) circadian related pathways. Network analysis further revealed that the mutated genes with the highest betweenness coefficients, such as the well-known cancer genes TP53, CTNNB1 and recently identified novel mutated genes GNAL and the ADCY family, may play key roles in these significantly mutated pathways. Finally, we highlight several key genes (e.g., RPS6KA3 and PCLO) and pathways (e.g., axon guidance) in which the mutations were associated with clinical features. Conclusions Our workflow illustrates the increased statistical power of integrating multiple studies of the same subject, which can provide biological insights that would otherwise be masked under individual sample sets. This type of bioinformatics approach is consistent with the necessity of making the best use of the ever increasing data provided in valuable databases, such as TCGA, to enhance the speed of deciphering human cancers. PMID:24988079

  11. Structure identifiability in metabolic pathways: parameter estimation in models based on the power-law formalism.

    PubMed Central

    Sorribas, A; Cascante, M

    1994-01-01

    An important step in understanding a metabolic pathway is to identify its structure, in terms of the flow of material and information. In pursuing this goal, the available information for a given system is usually obtained from experiments in vitro and comes from different sources. Frequently, the final set of regulatory signals acting in the system in vivo is unclear, and some kind of test is needed on the intact system. Besides defining an appropriate experimental approach, identification of the regulatory pattern needs a theoretical framework in which the different experimental measurements can be evaluated and a final picture can be agreed on. Mathematical approaches based on sensitivity coefficients provide a useful tool for addressing this problem. Within this framework, the appropriate parameters are related to both the structure of the reaction network and the signals that regulate the target system. Thus the identification of the regulatory structure can be related to the estimation of the appropriate set of parameters. In pursuing this goal, we will show the limitations of using steady-state measurements and the usefulness of using dynamic data. We suggest a way to test the regulatory pattern in a given metabolic pathway by combining both kinds of data, and we show, by using a reference system, the potential of the method suggested. PMID:8135735

  12. 2D NMR-based metabolomics uncovers interactions between conserved biochemical pathways in the model organism Caenorhabditis elegans.

    PubMed

    Izrayelit, Yevgeniy; Robinette, Steven L; Bose, Neelanjan; von Reuss, Stephan H; Schroeder, Frank C

    2013-02-15

    Ascarosides are small-molecule signals that play a central role in C. elegans biology, including dauer formation, aging, and social behaviors, but many aspects of their biosynthesis remain unknown. Using automated 2D NMR-based comparative metabolomics, we identified ascaroside ethanolamides as shunt metabolites in C. elegans mutants of daf-22, a gene with homology to mammalian 3-ketoacyl-CoA thiolases predicted to function in conserved peroxisomal lipid ?-oxidation. Two groups of ethanolamides feature ?-keto functionalization confirming the predicted role of daf-22 in ascaroside biosynthesis, whereas ?-methyl substitution points to unexpected inclusion of methylmalonate at a late stage in the biosynthesis of long-chain fatty acids in C. elegans. We show that ascaroside ethanolamide formation in response to defects in daf-22 and other peroxisomal genes is associated with severe depletion of endocannabinoid pools. These results indicate unexpected interaction between peroxisomal lipid ?-oxidation and the biosynthesis of endocannabinoids, which are major regulators of lifespan in C. elegans. Our study demonstrates the utility of unbiased comparative metabolomics for investigating biochemical networks in metazoans. PMID:23163760

  13. Long-term recovery from hippocampal-related behavioral and biochemical abnormalities induced by noise exposure during brain development. Evaluation of auditory pathway integrity.

    PubMed

    Uran, S L; Gómez-Casati, M E; Guelman, L R

    2014-10-01

    Sound is an important part of man's contact with the environment and has served as critical means for survival throughout his evolution. As a result of exposure to noise, physiological functions such as those involving structures of the auditory and non-auditory systems might be damaged. We have previously reported that noise-exposed developing rats elicited hippocampal-related histological, biochemical and behavioral changes. However, no data about the time lapse of these changes were reported. Moreover, measurements of auditory pathway function were not performed in exposed animals. Therefore, with the present work, we aim to test the onset and the persistence of the different extra-auditory abnormalities observed in noise-exposed rats and to evaluate auditory pathway integrity. Male Wistar rats of 15 days were exposed to moderate noise levels (95-97 dB SPL, 2 h a day) during one day (acute noise exposure, ANE) or during 15 days (sub-acute noise exposure, SANE). Hippocampal biochemical determinations as well as short (ST) and long term (LT) behavioral assessments were performed. In addition, histological and functional evaluations of the auditory pathway were carried out in exposed animals. Our results show that hippocampal-related behavioral and biochemical changes (impairments in habituation, recognition and associative memories as well as distortion of anxiety-related behavior, decreases in reactive oxygen species (ROS) levels and increases in antioxidant enzymes activities) induced by noise exposure were almost completely restored by PND 90. In addition, auditory evaluation shows that increased cochlear thresholds observed in exposed rats were re-established at PND 90, although with a remarkable supra-threshold amplitude reduction. These data suggest that noise-induced hippocampal and auditory-related alterations are mostly transient and that the effects of noise on the hippocampus might be, at least in part, mediated by the damage on the auditory pathway. However, we cannot exclude that a different mechanism might be responsible for the observed hippocampal-related changes. PMID:24911434

  14. Cross-platform pathway-based analysis identifies markers of response to the PARP inhibitor olaparib.

    PubMed

    Daemen, Anneleen; Wolf, Denise M; Korkola, James E; Griffith, Obi L; Frankum, Jessica R; Brough, Rachel; Jakkula, Lakshmi R; Wang, Nicholas J; Natrajan, Rachael; Reis-Filho, Jorge S; Lord, Christopher J; Ashworth, Alan; Spellman, Paul T; Gray, Joe W; van't Veer, Laura J

    2012-09-01

    Poly(ADP-ribose) polymerase (PARP) is an enzyme involved in DNA repair. PARP inhibitors can act as chemosensitizers, or operate on the principle of synthetic lethality when used as single agent. Clinical trials have shown drugs in this class to be promising for BRCA mutation carriers. We postulated that inability to demonstrate response in non-BRCA carriers in which BRCA is inactivated by other mechanisms or with deficiency in homologous recombination for DNA repair is due to lack of molecular markers that define a responding subpopulation. We identified candidate markers for this purpose for olaparib (AstraZeneca) by measuring inhibitory effects of nine concentrations of olaparib in 22 breast cancer cell lines and identifying features in transcriptional and genome copy number profiles that were significantly correlated with response. We emphasized in this discovery process genes involved in DNA repair. We found that the cell lines that were sensitive to olaparib had a significant lower copy number of BRCA1 compared to the resistant cell lines (p value 0.012). In addition, we discovered seven genes from DNA repair pathways whose transcriptional levels were associated with response. These included five genes (BRCA1, MRE11A, NBS1, TDG, and XPA) whose transcript levels were associated with resistance and two genes (CHEK2 and MK2) whose transcript levels were associated with sensitivity. We developed an algorithm to predict response using the seven-gene transcription levels and applied it to 1,846 invasive breast cancer samples from 8 U133A/plus 2 (Affymetrix) data sets and found that 8-21 % of patients would be predicted to be responsive to olaparib. A similar response frequency was predicted in 536 samples analyzed on an Agilent platform. Importantly, tumors predicted to respond were enriched in basal subtype tumors. Our studies support clinical evaluation of the utility of our seven-gene signature as a predictor of response to olaparib. PMID:22875744

  15. Pathways to obesity: identifying local, modifiable determinants of physical activity and diet.

    PubMed

    Stafford, Mai; Cummins, Steven; Ellaway, Anne; Sacker, Amanda; Wiggins, Richard D; Macintyre, Sally

    2007-11-01

    Many studies document small area inequalities in morbidity and mortality and show associations between area deprivation and health. However, few studies unpack the "black box" of area deprivation to show which specific local social and physical environmental characteristics impact upon health, and might be amenable to modification. We theorised a model of the potential causal pathways to obesity and employed path analysis using a rich data set from national studies in England and Scotland to test the model empirically. Significant associations between obesity and neighbourhood disorder and access to local high street facilities (local shops, financial services and health-related stores found in a typical small UK town) were found. There was a tendency for lower levels of obesity in areas with more swimming pools and supermarkets. In turn, policing levels, physical dereliction and recorded violent crime were associated with neighbourhood disorder. The analysis identifies several factors that are associated with (and are probably determinants of) obesity and which are outside the standard remit of the healthcare sector. They highlight the role that public and private sector organisations have in promoting the nation's health. Public health professionals should seek to work alongside or within these organisations to capitalise on opportunities to improve health. PMID:17640787

  16. Selective ?v integrin depletion identifies a core, targetable molecular pathway that regulates fibrosis across solid organs

    PubMed Central

    Henderson, Neil C; Arnold, Thomas D; Katamura, Yoshio; Giacomini, Marilyn M; Rodriguez, Juan D; McCarty, Joseph H; Pellicoro, Antonella; Raschperger, Elisabeth; Betsholtz, Christer; Ruminski, Peter G; Griggs, David W; Prinsen, Michael J; Maher, Jacquelyn J; Iredale, John P; Lacy-Hulbert, Adam; Adams, Ralf H; Sheppard, Dean

    2013-01-01

    Myofibroblasts are the major source of extracellular matrix components that accumulate during tissue fibrosis, and hepatic stellate cells (HSCs) are the major source of myofibroblasts in the liver. To date, robust systems to genetically manipulate these cells have not existed. We report that Pdgfrb-Cre inactivates genes in murine HSCs with high efficiency. We used this system to delete the ?v integrin subunit because of the suggested role of multiple ?v integrins as central mediators of fibrosis in multiple organs. Depletion of the ?v integrin subunit in HSCs protected mice from CCl4-induced hepatic fibrosis, whereas global loss of ?v?3, ?v?5 or ?v?6 or conditional loss of ?v?8 on HSCs did not. Pdgfrb-Cre effectively targeted myofibroblasts in multiple organs, and depletion of ?v integrins using this system was also protective in models of pulmonary and renal fibrosis. Critically, pharmacological blockade of ?v integrins by a novel small molecule (CWHM 12) attenuated both liver and lung fibrosis, even when administered after fibrosis was established. These data identify a core pathway that regulates fibrosis, and suggest that pharmacological targeting of all ?v integrins may have clinical utility in the treatment of patients with a broad range of fibrotic diseases. PMID:24216753

  17. Identifying specific profiles in patients with different degrees of painful knee osteoarthritis based on serological biochemical and mechanistic pain biomarkers: a diagnostic approach based on cluster analysis.

    PubMed

    Egsgaard, Line Lindhardt; Eskehave, Thomas Navndrup; Bay-Jensen, Anne C; Hoeck, Hans Christian; Arendt-Nielsen, Lars

    2015-01-01

    Biochemical and pain biomarkers can be applied to patients with painful osteoarthritis profiles and may provide more details compared with conventional clinical tools. The aim of this study was to identify an optimal combination of biochemical and pain biomarkers for classification of patients with different degrees of knee pain and joint damage. Such profiling may provide new diagnostic and therapeutic options. A total of 216 patients with different degrees of knee pain (maximal pain during the last 24 hours rated on a visual analog scale [VAS]) (VAS 0-100) and 64 controls (VAS 0-9) were recruited. Patients were separated into 3 groups: VAS 10 to 39 (N = 81), VAS 40 to 69 (N = 70), and VAS 70 to 100 (N = 65). Pressure pain thresholds, temporal summation to pressure stimuli, and conditioning pain modulation were measured from the peripatellar and extrasegmental sites. Biochemical markers indicative for autoinflammation and immunity (VICM, CRP, and CRPM), synovial inflammation (CIIIM), cartilage loss (CIIM), and bone degradation (CIM) were analyzed. WOMAC, Lequesne, and pain catastrophizing scores were collected. Principal component analysis was applied to select the optimal variable subset, and cluster analysis was applied to this subset to create distinctly different knee pain profiles. Four distinct knee pain profiles were identified: profile A (N = 27), profile B (N = 59), profile C (N = 85), and profile D (N = 41). Each knee pain profile had a unique combination of biochemical markers, pain biomarkers, physical impairments, and psychological factors that may provide the basis for mechanism-based diagnosis, individualized treatment, and selection of patients for clinical trials evaluating analgesic compounds. These results introduce a new profiling for knee OA and should be regarded as preliminary. PMID:25599306

  18. Genetic analysis of the two zebrafish patched homologues identifies novel roles for the hedgehog signaling pathway

    Microsoft Academic Search

    Marco J Koudijs; Marjo J den Broeder; Evelyn Groot; Fredericus JM van Eeden

    2008-01-01

    BACKGROUND: Aberrant activation of the Hedgehog (Hh) signaling pathway in different organisms has shown the importance of this family of morphogens during development. Genetic screens in zebrafish have assigned specific roles for Hh in proliferation, differentiation and patterning, but mainly as a result of a loss of its activity. We attempted to fully activate the Hh pathway by removing both

  19. Dual pathways to endochondral osteoblasts: a novel chondrocyte-derived osteoprogenitor cell identified in hypertrophic cartilage

    PubMed Central

    Park, Jung; Gebhardt, Matthias; Golovchenko, Svitlana; Perez-Branguli, Francesc; Hattori, Takako; Hartmann, Christine; Zhou, Xin; deCrombrugghe, Benoit; Stock, Michael; Schneider, Holm; von der Mark, Klaus

    2015-01-01

    According to the general understanding, the chondrocyte lineage terminates with the elimination of late hypertrophic cells by apoptosis in the growth plate. However, recent cell tracking studies have shown that murine hypertrophic chondrocytes can survive beyond “terminal” differentiation and give rise to a progeny of osteoblasts participating in endochondral bone formation. The question how chondrocytes convert into osteoblasts, however, remained open. Following the cell fate of hypertrophic chondrocytes by genetic lineage tracing using BACCol10;Cre induced YFP-reporter gene expression we show that a progeny of Col10Cre-reporter labelled osteoprogenitor cells and osteoblasts appears in the primary spongiosa and participates – depending on the developmental stage – substantially in trabecular, endosteal, and cortical bone formation. YFP+ trabecular and endosteal cells isolated by FACS expressed Col1a1, osteocalcin and runx2, thus confirming their osteogenic phenotype. In searching for transitory cells between hypertrophic chondrocytes and trabecular osteoblasts we identified by confocal microscopy a novel, small YFP+Osx+ cell type with mitotic activity in the lower hypertrophic zone at the chondro-osseous junction. When isolated from growth plates by fractional enzymatic digestion, these cells termed CDOP (chondrocyte-derived osteoprogenitor) cells expressed bone typical genes and differentiated into osteoblasts in vitro. We propose the Col10Cre-labeled CDOP cells mark the initiation point of a second pathway giving rise to endochondral osteoblasts, alternative to perichondrium derived osteoprogenitor cells. These findings add to current concepts of chondrocyte-osteocyte lineages and give new insight into the complex cartilage-bone transition process in the growth plate. PMID:25882555

  20. Genome-Wide Expression Profiling Identifies Type 1 Interferon Response Pathways in Active Tuberculosis

    PubMed Central

    Ottenhoff, Tom H. M.; Zhang, Mingzi M.; Wong, Hazel E. E.; Sahiratmadja, Edhyana; Khor, Chiea Chuen; Alisjahbana, Bachti; van Crevel, Reinout; Marzuki, Sangkot; Seielstad, Mark; van de Vosse, Esther; Hibberd, Martin L.

    2012-01-01

    Tuberculosis (TB), caused by Mycobacterium tuberculosis (M.tb), remains the leading cause of mortality from a single infectious agent. Each year around 9 million individuals newly develop active TB disease, and over 2 billion individuals are latently infected with M.tb worldwide, thus being at risk of developing TB reactivation disease later in life. The underlying mechanisms and pathways of protection against TB in humans, as well as the dynamics of the host response to M.tb infection, are incompletely understood. We carried out whole-genome expression profiling on a cohort of TB patients longitudinally sampled along 3 time-points: during active infection, during treatment, and after completion of curative treatment. We identified molecular signatures involving the upregulation of type-1 interferon (?/?) mediated signaling and chronic inflammation during active TB disease in an Indonesian population, in line with results from two recent studies in ethnically and epidemiologically different populations in Europe and South Africa. Expression profiles were captured in neutrophil-depleted blood samples, indicating a major contribution of lymphocytes and myeloid cells. Expression of type-1 interferon (?/?) genes mediated was also upregulated in the lungs of M.tb infected mice and in infected human macrophages. In patients, the regulated gene expression-signature normalized during treatment, including the type-1 interferon mediated signaling and a concurrent opposite regulation of interferon-gamma. Further analysis revealed IL15RA, UBE2L6 and GBP4 as molecules involved in the type-I interferon response in all three experimental models. Our data is highly suggestive that the innate immune type-I interferon signaling cascade could be used as a quantitative tool for monitoring active TB disease, and provide evidence that components of the patient’s blood gene expression signature bear similarities to the pulmonary and macrophage response to mycobacterial infection. PMID:23029268

  1. Avian Botulism in Distressed Great Lakes Environments pathways in the food chain, and identifying physical and biological

    E-print Network

    Avian Botulism in Distressed Great Lakes Environments pathways in the food chain, and identifying to break linkages that lead to botulism outbreaks. Habitat and Wildlife Protection and Restoration Projects for the Great Lakes Restoration Initiative ·An assay was developed to detect type-E botulism toxin (Bo

  2. Genome Regions Involved in Multiple Regulatory Pathways Identified Using GSEL, a Genome-Wide Database of Regulatory Sequence Elements of

    E-print Network

    Lovley, Derek

    Genome Regions Involved in Multiple Regulatory Pathways Identified Using GSEL, a Genome://www.geobacter.org/research/gsel/). It compiles information on predicted transcription regulatory elements in the genome of G. sulfurreducens. These elements were derived from analyses that employed genome-wide transcription profiling, comparative genomics

  3. A novel method to identify pathways associated with renal cell carcinoma based on a gene co-expression network.

    PubMed

    Ruan, Xiyun; Li, Hongyun; Liu, Bo; Chen, Jie; Zhang, Shibao; Sun, Zeqiang; Liu, Shuangqing; Sun, Fahai; Liu, Qingyong

    2015-08-01

    The aim of the present study was to develop a novel method for identifying pathways associated with renal cell carcinoma (RCC) based on a gene co-expression network. A framework was established where a co-expression network was derived from the database as well as various co-expression approaches. First, the backbone of the network based on differentially expressed (DE) genes between RCC patients and normal controls was constructed by the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database. The differentially co-expressed links were detected by Pearson's correlation, the empirical Bayesian (EB) approach and Weighted Gene Co-expression Network Analysis (WGCNA). The co-expressed gene pairs were merged by a rank?based algorithm. We obtained 842; 371; 2,883 and 1,595 co-expressed gene pairs from the co-expression networks of the STRING database, Pearson's correlation EB method and WGCNA, respectively. Two hundred and eighty?one differentially co-expressed (DC) gene pairs were obtained from the merged network using this novel method. Pathway enrichment analysis based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and the network enrichment analysis (NEA) method were performed to verify feasibility of the merged method. Results of the KEGG and NEA pathway analyses showed that the network was associated with RCC. The suggested method was computationally efficient to identify pathways associated with RCC and has been identified as a useful complement to traditional co-expression analysis. PMID:26058425

  4. Acute Myeloid Leukemia Subgroups Identified by Pathway-Restricted Gene Expression Signatures

    Microsoft Academic Search

    Elena Serrano; Adriana Lasa; Granada Perea; Maria J. Carnicer; Salut Brunet; Anna Aventín; Jorge Sierra; Josep F. Nomdedéu

    2006-01-01

    Acute myeloid leukemia (AML) is a heterogeneous group of disorders characterized by abnormal proliferation of myeloid precursors and a maturation block. Underlying genetic lesions determine an altered expression program (transcriptosome) that can be studied in depth by massive technologies. Alternatively, we selected a pathway profiling strategy based on the current knowledge in order to stratify de novo AML patients and

  5. Identifying the Causal Pathways from Religiosity to Delayed Adolescent Sexual Behavior

    Microsoft Academic Search

    Shawnika J. Hull; Michael Hennessy; Amy Bleakley; Martin Fishbein; Amy Jordan

    2010-01-01

    This study used the Integrative Model as a framework to examine whether religiosity delays onset of coitus among a longitudinal sample of virgins, and investigated the causal pathways of this relationship. In addition, this study examined the behavioral beliefs about the consequences of engaging in sex, which distinguishes between youth who vary in level of religiosity. A further analysis was

  6. Identifying the Causal Pathways from Religiosity to Delayed Adolescent Sexual Behavior

    Microsoft Academic Search

    Shawnika J. Hull; Michael Hennessy; Amy Bleakley; Martin Fishbein; Amy Jordan

    2011-01-01

    This study used the Integrative Model as a framework to examine whether religiosity delays onset of coitus among a longitudinal sample of virgins, and investigated the causal pathways of this relationship. In addition, this study examined the behavioral beliefs about the consequences of engaging in sex, which distinguishes between youth who vary in level of religiosity. A further analysis was

  7. UTSW Investigators Develop Functional Signature Ontology (FUSION), a Method for Identifying Compounds That Target Cancer Pathways

    Cancer.gov

    In a new study published in Science Signaling, CTD2 investigators from University of Texas (UTSW) Southwestern Medical Center devised a novel bioinformatics approach that, when coupled with high-throughput screening, helps reveal compounds that may target potential cancer-related pathways.

  8. Biochemical characterization of the O-linked glycosylation pathway in Neisseria gonorrhoeae responsible for biosynthesis of protein glycans containing N,N’-diacetylbacillosamine†

    PubMed Central

    Hartley, Meredith D.; Morrison, Michael J.; Aas, Finn Erik; Børud, Bente; Koomey, Michael; Imperiali, Barbara

    2011-01-01

    The O-linked protein glycosylation pathway in Neisseria gonorrhoeae is responsible for the synthesis of a complex oligosaccharide on undecaprenyl diphosphate and subsequent en bloc transfer of the glycan to serine residues of select periplasmic proteins. Protein glycosylation (pgl) genes have been annotated on the basis of bioinformatics and top-down mass spectrometry analysis of protein modifications in pgl-null strains (1, 2), but relatively little biochemical analysis has been performed to date. In this report, we present the expression, purification and functional characterization of seven Pgl enzymes. Specifically, the enzymes studied are responsible for synthesis of an uncommon uridine diphosphate (UDP)-sugar (PglD, PglC, and PglB-acetyltransferase domain), glycan assembly (PglB-phospho-glycosyltransferase domain, PglA, PglE, and PglH) and final oligosaccharide transfer (PglO). UDP-2,4-diacetamido-2,4,6-trideoxy-?-D-hexose (DATDH), which is the first sugar in glycan biosynthesis, was produced enzymatically and the stereochemistry was assigned as uridine diphosphate N’-diacetylbacillosamine (UDP-diNAcBac) by NMR characterization. In addition, the substrate specificities of the phospho-glycosyltransferase, glycosyltransferases and oligosaccharyltransferase (OTase) were analyzed in vitro and in most cases, these enzymes showed strong preferences for the native substrates relative to closely related glycans. In particular, PglO, the O-linked OTase, and PglB(Cj), the N-linked OTase from Campylobacter jejuni, preferred the native N. gonorrhoeae or C. jejuni substrates, respectively. This study represents the first comprehensive biochemical characterization of this important O-linked glycosylation pathway and provides the basis for further investigations of these enzymes as antibacterial targets. PMID:21542610

  9. Genetic analysis of the two zebrafish patched homologues identifies novel roles for the hedgehog signaling pathway

    PubMed Central

    Koudijs, Marco J; den Broeder, Marjo J; Groot, Evelyn; van Eeden, Fredericus JM

    2008-01-01

    Background Aberrant activation of the Hedgehog (Hh) signaling pathway in different organisms has shown the importance of this family of morphogens during development. Genetic screens in zebrafish have assigned specific roles for Hh in proliferation, differentiation and patterning, but mainly as a result of a loss of its activity. We attempted to fully activate the Hh pathway by removing both receptors for the Hh proteins, called Patched1 and 2, which are functioning as negative regulators in this pathway. Results Here we describe a splice-donor mutation in Ptc1, called ptc1hu1602, which in a homozygous state results in a subtle eye and somite phenotype. Since we recently positionally cloned a ptc2 mutant, a ptc1;ptc2 double mutant was generated, showing severely increased levels of ptc1, gli1 and nkx2.2a, confirming an aberrant activation of Hh signaling. As a consequence, a number of phenotypes were observed that have not been reported previously using Shh mRNA overexpression. Somites of ptc1;ptc2 double mutants do not express anteroposterior polarity markers, however initial segmentation of the somites itself is not affected. This is the first evidence that segmentation and anterior/posterior (A/P) patterning of the somites are genetically uncoupled processes. Furthermore, a novel negative function of Hh signaling is observed in the induction of the fin field, acting well before any of the previously reported function of Shh in fin formation and in a way that is different from the proposed early role of Gli3 in limb/fin bud patterning. Conclusion The generation and characterization of the ptc1;ptc2 double mutant assigned novel and unexpected functions to the Hh signaling pathway. Additionally, these mutants will provide a useful system to further investigate the consequences of constitutively activated Hh signaling during vertebrate development. PMID:18284698

  10. Two-dimensional speckle tracking imaging as a novel strategy for accurately identifying the accessory pathway.

    PubMed

    Iwayama, Tadateru; Arimoto, Takanori; Tamura, Harutoshi; Wanezaki, Masahiro; Sasaki, Shintaro; Nishiyama, Satoshi; Kutsuzawa, Daisuke; Ishigaki, Daisuke; Nitobe, Joji; Suzuki, Hiroshi; Watanabe, Tetsu; Kubota, Isao

    2014-01-01

    A 14-year-old patient was diagnosed with hypertrophic cardiomyopathy associated with Wolff-Parkinson-White syndrome. The two-dimensional speckle tracking strain method showed normal left ventricular local contraction, but the peak systolic longitudinal strain of the right ventricular (RV) anterior wall was earlier than that of the septal wall. As expected, the location of the accessory pathway was at the RV anterior wall. The patient's RV local contraction was normalized by successful radiofrequency application. PMID:25030566

  11. An evidence-based knowledgebase of pulmonary arterial hypertension to identify genes and pathways relevant to pathogenesis.

    PubMed

    Zhao, Min; Austin, Eric D; Hemnes, Anna R; Loyd, James E; Zhao, Zhongming

    2014-04-01

    Pulmonary arterial hypertension (PAH) is a major progressive form of pulmonary hypertension (PH) with more than 4800 patients in the United States. In the last two decades, many studies have identified numerous genes associated with this disease. However, there is no comprehensive research resource for PAH or other PH types that integrates various genetic studies and their related biological information. Thus, the number of associated genes, and their strength of evidence, is unclear. In this study, we tested the hypothesis that a web-based knowledgebase could be used to develop a biological map of highly interrelated, functionally important genes in PAH. We developed the pulmonary arterial hypertension knowledgebase (PAHKB, ), a comprehensive database with a user-friendly web interface. PAHKB extracts genetic data from all available sources, including those from association studies, genetic mutation, gene expression, animal model, supporting literature, various genomic annotations, gene networks, cellular and regulatory pathways, as well as microRNAs. Moreover, PAHKB provides online tools for data browsing and searching, data integration, pathway graphical presentation, and gene ranking. In the current release, PAHKB contains 341 human PH-related genes (293 protein coding and 48 non-coding genes) curated from over 1000 PubMed abstracts. Based on the top 39 ranked PAH-related genes in PAHKB, we constructed a core biological map. This core map was enriched with the TGF-beta signaling pathway, focal adhesion, cytokine-cytokine receptor interaction, and MAPK signaling. In addition, the reconstructed map elucidates several novel cancer signaling pathways, which may provide clues to support the application of anti-cancer therapeutics to PAH. In summary, we have developed a system for the identification of core PH-related genes and identified critical signaling pathways that may be relevant to PAH pathogenesis. This system can be easily applied to other pulmonary diseases. PMID:24448676

  12. Structural and biochemical studies identify tobacco SABP2 as a methyl salicylate esterase and implicate it in plant innate immunity

    Microsoft Academic Search

    Farhad Forouhar; Yue Yang; Dhirendra Kumar; Yang Chen; Eyal Fridman; Sang Wook Park; Yiwen Chiang; Thomas B. Acton; Gaetano T. Montelione; Eran Pichersky; Daniel F. Klessig; Liang Tong

    2005-01-01

    Salicylic acid (SA) is a critical signal for the activation of plant defense responses against pathogen infections. We recently identified SA-binding protein 2 (SABP2) from tobacco as a protein that displays high affinity for SA and plays a crucial role in the activation of systemic acquired resistance to plant pathogens. Here we report the crystal structures of SABP2, alone and

  13. A genomewide overexpression screen identifies genes involved in the phosphatidylinositol 3-kinase pathway in the human protozoan parasite Entamoeba histolytica.

    PubMed

    Koushik, Amrita B; Welter, Brenda H; Rock, Michelle L; Temesvari, Lesly A

    2014-03-01

    Entamoeba histolytica is a protozoan parasite that causes amoebic dysentery and liver abscess. E. histolytica relies on motility, phagocytosis, host cell adhesion, and proteolysis of extracellular matrix for virulence. In eukaryotic cells, these processes are mediated in part by phosphatidylinositol 3-kinase (PI3K) signaling. Thus, PI3K may be critical for virulence. We utilized a functional genomics approach to identify genes whose products may operate in the PI3K pathway in E. histolytica. We treated a population of trophozoites that were overexpressing genes from a cDNA library with a near-lethal dose of the PI3K inhibitor wortmannin. This screen was based on the rationale that survivors would be overexpressing gene products that directly or indirectly function in the PI3K pathway. We sequenced the overexpressed genes in survivors and identified a cDNA encoding a Rap GTPase, a protein previously shown to participate in the PI3K pathway. This supports the validity of our approach. Genes encoding a coactosin-like protein, EhCoactosin, and a serine-rich E. histolytica protein (SREHP) were also identified. Cells overexpressing EhCoactosin or SREHP were also less sensitive to a second PI3K inhibitor, LY294002. This corroborates the link between these proteins and PI3K. Finally, a mutant cell line with an increased level of phosphatidylinositol (3,4,5)-triphosphate, the product of PI3K activity, exhibited increased expression of SREHP and EhCoactosin. This further supports the functional connection between these proteins and PI3K in E. histolytica. To our knowledge, this is the first forward-genetics screen adapted to reveal genes participating in a signal transduction pathway in this pathogen. PMID:24442890

  14. A Genomewide Overexpression Screen Identifies Genes Involved in the Phosphatidylinositol 3-Kinase Pathway in the Human Protozoan Parasite Entamoeba histolytica

    PubMed Central

    Koushik, Amrita B.; Welter, Brenda H.; Rock, Michelle L.

    2014-01-01

    Entamoeba histolytica is a protozoan parasite that causes amoebic dysentery and liver abscess. E. histolytica relies on motility, phagocytosis, host cell adhesion, and proteolysis of extracellular matrix for virulence. In eukaryotic cells, these processes are mediated in part by phosphatidylinositol 3-kinase (PI3K) signaling. Thus, PI3K may be critical for virulence. We utilized a functional genomics approach to identify genes whose products may operate in the PI3K pathway in E. histolytica. We treated a population of trophozoites that were overexpressing genes from a cDNA library with a near-lethal dose of the PI3K inhibitor wortmannin. This screen was based on the rationale that survivors would be overexpressing gene products that directly or indirectly function in the PI3K pathway. We sequenced the overexpressed genes in survivors and identified a cDNA encoding a Rap GTPase, a protein previously shown to participate in the PI3K pathway. This supports the validity of our approach. Genes encoding a coactosin-like protein, EhCoactosin, and a serine-rich E. histolytica protein (SREHP) were also identified. Cells overexpressing EhCoactosin or SREHP were also less sensitive to a second PI3K inhibitor, LY294002. This corroborates the link between these proteins and PI3K. Finally, a mutant cell line with an increased level of phosphatidylinositol (3,4,5)-triphosphate, the product of PI3K activity, exhibited increased expression of SREHP and EhCoactosin. This further supports the functional connection between these proteins and PI3K in E. histolytica. To our knowledge, this is the first forward-genetics screen adapted to reveal genes participating in a signal transduction pathway in this pathogen. PMID:24442890

  15. Biological Biochemical Image Database

    NSDL National Science Digital Library

    The National Institute on Aging -- one of the National Institutes of Health -- provides the Biological Biochemical Image Database, "a searchable database of images of putative biological pathways, macromolecular structures, gene families, and cellular relationships." The database is intended for researchers "working with large sets of genes or proteins using cDNA arrays, functional genomics, or proteomics." The database may be searched by gene name, pathway, cell or tissue type, disease name, biological level, etc. Database users are invited to submit additional diagrams, suggestions, and comments The Web site also includes convenient lists of gene names and keywords, as well as links to biological/ biochemical pathway Web resources.

  16. The Prognostic Value of the Apoptosis Pathway in Colorectal Cancer: A Review of the Literature on Biomarkers Identified by Immunohistochemistry

    PubMed Central

    Zeestraten, Eliane C.M.; Benard, Anne; Reimers, Marlies S.; Schouten, Philip C.; Liefers, Gerrit J.; van de Velde, Cornelis J.H.; Kuppen, Peter J.K.

    2013-01-01

    Research towards biomarkers that predict patient outcome in colorectal cancer (CRC) is rapidly expanding. However, none of these biomarkers have been recommended by the American Association of Clinical Oncology or the European Group on Tumor Markers. Current staging criteria result in substantial under-and over-treatment of CRC patients. Evasion of apoptosis, a characteristic feature of tumorigenesis, is known to correlate with patient outcome. We reviewed the literature on immunohistochemistry-based studies between 1998 and 2011 describing biomarkers in this pathway in CRC and identified 26 markers. Most frequently described were p53, Bcl-2, survivin, and the Fas and TRAILR1 receptors and their ligands. None of the studies reviewed provided sufficient support for implementing a single marker into current clinical practice. This is likely due to the complex biology of this pathway. We suggest focusing on the combination of key markers within the apoptosis pathway that together represent an ‘apoptotic tumor profile’, which better reflects the status of this pathway in a tumor. PMID:24179395

  17. Gene expression profiling identifies emerging oncogenic pathways operating in extranodal NK/T-cell lymphoma, nasal type

    PubMed Central

    Huang, Yenlin; de Reyniès, Aurélien; de Leval, Laurence; Ghazi, Bouchra; Martin-Garcia, Nadine; Travert, Marion; Bosq, Jacques; Brière, Josette; Petit, Barbara; Thomas, Emilie; Coppo, Paul; Marafioti, Teresa; Emile, Jean-François; Delfau-Larue, Marie-Hélène; Schmitt, Christian

    2010-01-01

    Biopsies and cell lines of natural killer/T-cell lymphoma, nasal type (NKTCL) were subject to combined gene expression profiling and array-based comparative genomic hybridization analyses. Compared with peripheral T-cell lymphoma, not otherwise specified, NKTCL had greater transcript levels for NK-cell and cytotoxic molecules, especially granzyme H. Compared with normal NKcells, tumors were closer to activated than resting cells and overexpressed several genes related to vascular biology, Epstein-Barr Virus–induced genes, and PDGFRA. Notably, platelet-derived growth factor receptor ? and its phosphorylated form were confirmed at the protein level, and in vitro the MEC04 NKTCL cell line was sensitive to imatinib. Deregulation of the AKT, Janus kinase–signal transducers and activators of transcription, and nuclear factor-?B pathways was corroborated by nuclear expression of phosphorylated AKT, signal transducers and activators of transcription 3, and RelA in NKTCL, and several deregulated genes in these pathways mapped to regions of recurrent copy number aberrations (AKT3 [1q44], IL6R [1q21.3], CCL2 [17q12], TNFRSF21 [6p12.3]). Several features of NKTCL uncovered by this analysis suggest perturbation of angiogenic pathways. Integrative analysis also evidenced deregulation of the tumor suppressor HACE1 in the frequently deleted 6q21 region. This study highlights emerging oncogenic pathways in NKTCL and identifies novel diagnostic and therapeutic targets. PMID:19965620

  18. Major carcinogenic pathways identified by gene expression analysis of peritoneal mesotheliomas following chemical treatment in F344 rats

    SciTech Connect

    Kim, Yongbaek [Environmental Toxicology Program, National Institute of Environmental Health Sciences, MD B3-08, 111 Alexander Drive, Research Triangle Park, NC 27709 (United States); Thai-Vu Ton [Environmental Toxicology Program, National Institute of Environmental Health Sciences, MD B3-08, 111 Alexander Drive, Research Triangle Park, NC 27709 (United States); De Angelo, Anthony B. [Environmental Protection Agency, Research Triangle Park, NC 27709 (United States); Morgan, Kevin [Aventis, Bridgewater, NJ 08807 (United States); Devereux, Theodora R. [Environmental Carcinogenesis Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709 (United States); Anna, Colleen [Environmental Carcinogenesis Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709 (United States); Collins, Jennifer B. [Microarray Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709 (United States); Paules, Richard S. [Microarray Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709 (United States); Crosby, Lynn M. [Wyeth Research, Chazy, NY 12921 (United States); Sills, Robert C. [Environmental Toxicology Program, National Institute of Environmental Health Sciences, MD B3-08, 111 Alexander Drive, Research Triangle Park, NC 27709 (United States)]. E-mail: sills@niehs.nih.gov

    2006-07-15

    This study was performed to characterize the gene expression profile and to identify the major carcinogenic pathways involved in rat peritoneal mesothelioma (RPM) formation following treatment of Fischer 344 rats with o-nitrotoluene (o-NT) or bromochloracetic acid (BCA). Oligo arrays, with over 20,000 target genes, were used to evaluate o-NT- and BCA-induced RPMs, when compared to a non-transformed mesothelial cell line (Fred-PE). Analysis using Ingenuity Pathway Analysis software revealed 169 cancer-related genes that were categorized into binding activity, growth and proliferation, cell cycle progression, apoptosis, and invasion and metastasis. The microarray data were validated by positive correlation with quantitative real-time RT-PCR on 16 selected genes including igf1, tgfb3 and nov. Important carcinogenic pathways involved in RPM formation included insulin-like growth factor 1 (IGF-1), p38 MAPkinase, Wnt/{beta}-catenin and integrin signaling pathways. This study demonstrated that mesotheliomas in rats exposed to o-NT- and BCA were similar to mesotheliomas in humans, at least at the cellular and molecular level.

  19. Biochemical Plant Responses to Ozone (IV. Cross-Induction of Defensive Pathways in Parsley (Petroselinum crispum L.) Plants).

    PubMed Central

    Eckey-Kaltenbach, H.; Ernst, D.; Heller, W.; Sandermann, H.

    1994-01-01

    Parsley (Petroselinum crispum L.) is known to respond to ultraviolet irradiation by the synthesis of flavone glycosides, whereas fungal or elicitor stress leads to the synthesis of furanocoumarin phytoalexins. We tested how these defensive pathways are affected by a single ozone treatment (200 nL L-1; 10 h). Assays were performed at the levels of transcripts, for enzyme activities, and for secondary products. The most rapid transcript accumulation was maximal at 3 h, whereas flavone glycosides and furanocoumarins were maximally induced at 12 and 24 h, respectively, after the start of ozone treatment. Ozone acted as a cross-inducer because the two distinct pathways were simultaneously induced. These results are consistent with the previously observed ozone induction of fungal and viral defense reactions in tobacco, spruce, and pine. PMID:12232062

  20. Microarray and Biochemical Analysis of Lovastatin-Induced Apoptosis of Squamous Cell Carcinomas

    Microsoft Academic Search

    Jim Dimitroulakos; Wilson H. Marhin; Jason Tokunaga; Jonathan Irishy; Patrick Gullaney; Linda Z. Penn; Suzanne Kamel-Reid

    2002-01-01

    We recently identified 3 - hydroxy - 3 - methylglutaryl coenzyme A (HMG -CoA ) reductase, the rate -limiting enzyme of the mevalonate pathway, as a potential therapeutic target of the head and neck squamous cell carcinomas ( HNSCC) and cervical carcinomas (CC ). The products of this complex biochemical pathway, including de novo cholesterol, are vital for a variety

  1. Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering

    Microsoft Academic Search

    Stefan Schuster; Thomas Dandekar; David A. Fell

    1999-01-01

    Rational metabolic engineering requires powerful theoretical methods such as pathway analysis, in which the topology of metabolic networks is considered. All metabolic capabilities in steady states are composed of elementary flux modes, which are minimal sets of enzymes that can each generate valid steady states. The modes of the fructose-2,6-bisphosphate cycle, the combined tricarboxylic-acid-cycle–glyoxylate-shunt system and tryptophan synthesis are used

  2. Transcellular transport of polymeric IgA in the rat hepatocyte: biochemical and morphological characterization of the transport pathway

    Microsoft Academic Search

    CRAIG A. HOPPE; TIMOTHY P. CONNOLLY; ANN L. HUBBARD

    1985-01-01

    Polymeric IgA (plgA) is transported by liver parenchymal cells (hepatocytes) from blood to bile via a receptor-mediated process. We have studied the intracellular pathway taken by a TEPC15 mouse myeioma plgA. When from 1 pg to 1 mg 12Sl-plgA was injected into the saphenous vein of a rat, 36% was transported as intact protein into the bile over a 3-h

  3. Metabolic, Genomic, and Biochemical Analyses of Glandular Trichomes from the Wild Tomato Species Lycopersicon hirsutum Identify a Key Enzyme in the Biosynthesis of MethylketonesW?

    PubMed Central

    Fridman, Eyal; Wang, Jihong; Iijima, Yoko; Froehlich, John E.; Gang, David R.; Ohlrogge, John; Pichersky, Eran

    2005-01-01

    Medium-length methylketones (C7-C15) are highly effective in protecting plants from numerous pests. We used a biochemical genomics approach to elucidate the pathway leading to synthesis of methylketones in the glandular trichomes of the wild tomato Lycopersicon hirsutum f glabratum (accession PI126449). A comparison of gland EST databases from accession PI126449 and a second L. hirsutum accession, LA1777, whose glands do not contain methylketones, showed that the expression of genes for fatty acid biosynthesis is elevated in PI126449 glands, suggesting de novo biosynthesis of methylketones. A cDNA abundant in the PI126449 gland EST database but rare in the LA1777 database was similar in sequence to plant esterases. This cDNA, designated Methylketone Synthase 1 (MKS1), was expressed in Escherichia coli and the purified protein used to catalyze in vitro reactions in which C12, C14, and C16 ?-ketoacyl–acyl-carrier-proteins (intermediates in fatty acid biosynthesis) were hydrolyzed and decarboxylated to give C11, C13, and C15 methylketones, respectively. Although MKS1 does not contain a classical transit peptide, in vitro import assays showed that it was targeted to the stroma of plastids, where fatty acid biosynthesis occurs. Levels of MKS1 transcript, protein, and enzymatic activity were correlated with levels of methylketones and gland density in a variety of tomato accessions and in different plant organs. PMID:15772286

  4. Structural and Biochemical Studies of the C-Terminal Domain of Mouse Peptide-N-glycanase Identify it as a Mannose-Binding Module

    SciTech Connect

    Zhou,X.; Zhao, G.; Truglio, J.; Wang, L.; Li, G.; Lennarz, W.; Schindelin, H.

    2006-01-01

    The inability of certain N-linked glycoproteins to adopt their native conformation in the endoplasmic reticulum (ER) leads to their retrotranslocation into the cytosol and subsequent degradation by the proteasome. In this pathway the cytosolic peptide-N-glycanase (PNGase) cleaves the N-linked glycan chains off denatured glycoproteins. PNGase is highly conserved in eukaryotes and plays an important role in ER-associated protein degradation. In higher eukaryotes, PNGase has an N-terminal and a C-terminal extension in addition to its central catalytic domain, which is structurally and functionally related to transglutaminases. Although the N-terminal domain of PNGase is involved in protein-protein interactions, the function of the C-terminal domain has not previously been characterized. Here, we describe biophysical, biochemical, and crystallographic studies of the mouse PNGase C-terminal domain, including visualization of a complex between this domain and mannopentaose. These studies demonstrate that the C-terminal domain binds to the mannose moieties of N-linked oligosaccharide chains, and we further show that it enhances the activity of the mouse PNGase core domain, presumably by increasing the affinity of mouse PNGase for the glycan chains of misfolded glycoproteins.

  5. Systems analysis of primary Sjögren's syndrome pathogenesis in salivary glands identifies shared pathways in human and a mouse model

    PubMed Central

    2012-01-01

    Introduction Primary Sjögren's syndrome (pSS) is a chronic autoimmune disease with complex etiopathogenesis. Despite extensive studies to understand the disease process utilizing human and mouse models, the intersection between these species remains elusive. To address this gap, we utilized a novel systems biology approach to identify disease-related gene modules and signaling pathways that overlap between humans and mice. Methods Parotid gland tissues were harvested from 24 pSS and 16 non-pSS sicca patients and 25 controls. For mouse studies, salivary glands were harvested from C57BL/6.NOD-Aec1Aec2 mice at various times during development of pSS-like disease. RNA was analyzed with Affymetrix HG U133+2.0 arrays for human samples and with MOE430+2.0 arrays for mouse samples. The images were processed with Affymetrix software. Weighted-gene co-expression network analysis was used to identify disease-related and functional pathways. Results Nineteen co-expression modules were identified in human parotid tissue, of which four were significantly upregulated and three were downregulated in pSS patients compared with non-pSS sicca patients and controls. Notably, one of the human disease-related modules was highly preserved in the mouse model, and was enriched with genes involved in immune and inflammatory responses. Further comparison between these two species led to the identification of genes associated with leukocyte recruitment and germinal center formation. Conclusion Our systems biology analysis of genome-wide expression data from salivary gland tissue of pSS patients and from a pSS mouse model identified common dysregulated biological pathways and molecular targets underlying critical molecular alterations in pSS pathogenesis. PMID:23116360

  6. Integrated genome-wide association, coexpression network, and expression single nucleotide polymorphism analysis identifies novel pathway in allergic rhinitis

    PubMed Central

    2014-01-01

    Background Allergic rhinitis is a common disease whose genetic basis is incompletely explained. We report an integrated genomic analysis of allergic rhinitis. Methods We performed genome wide association studies (GWAS) of allergic rhinitis in 5633 ethnically diverse North American subjects. Next, we profiled gene expression in disease-relevant tissue (peripheral blood CD4+ lymphocytes) collected from subjects who had been genotyped. We then integrated the GWAS and gene expression data using expression single nucleotide (eSNP), coexpression network, and pathway approaches to identify the biologic relevance of our GWAS. Results GWAS revealed ethnicity-specific findings, with 4 genome-wide significant loci among Latinos and 1 genome-wide significant locus in the GWAS meta-analysis across ethnic groups. To identify biologic context for these results, we constructed a coexpression network to define modules of genes with similar patterns of CD4+ gene expression (coexpression modules) that could serve as constructs of broader gene expression. 6 of the 22 GWAS loci with P-value???1x10?6 tagged one particular coexpression module (4.0-fold enrichment, P-value 0.0029), and this module also had the greatest enrichment (3.4-fold enrichment, P-value 2.6?×?10?24) for allergic rhinitis-associated eSNPs (genetic variants associated with both gene expression and allergic rhinitis). The integrated GWAS, coexpression network, and eSNP results therefore supported this coexpression module as an allergic rhinitis module. Pathway analysis revealed that the module was enriched for mitochondrial pathways (8.6-fold enrichment, P-value 4.5?×?10?72). Conclusions Our results highlight mitochondrial pathways as a target for further investigation of allergic rhinitis mechanism and treatment. Our integrated approach can be applied to provide biologic context for GWAS of other diseases. PMID:25085501

  7. Microarray analysis of perichondral and reserve growth plate zones identifies differential gene expressions and signal pathways.

    PubMed

    Zhang, Mingliang; Pritchard, Meredith R; Middleton, Frank A; Horton, Jason A; Damron, Timothy A

    2008-09-01

    In the growth plate, the reserve and perichondral zones have been hypothesized to have similar functions, but their exact functions are poorly understood. Our hypothesis was that significant differential gene expression exists between perichondral and reserve chondrocytes that may differentiate the respective functions of these two zones. Normal Sprague-Dawley rat growth plate chondrocytes from the perichondral zone (PC) and reserve zone (RZ) were isolated by laser microdissection and then subjected to microarray analysis. In order to most comprehensively capture the unique features of the two zones, we analyzed both the most highly expressed genes and those that were most significantly different from the proliferative zone (PZ) as a single comparator. Confirmation of the differential expression of selected genes was done by quantitative real-time RT-PCR. A total of 8 transcripts showing high expression unique to the PC included translationally-controlled tumor protein (Tpt1), connective tissue growth factor (Ctgf), mortality factor 4 (Morf4l1), growth arrest specific 6 (Gas6), type V procollagen (Col5a2), frizzled-related protein (Frzb), GDP-dissociation inhibitor 2 (Gdi2) and Jun D proto-oncogene (Jund). In contrast, 8 transcripts showing unique high expression in the RZ included hyaluronan and proteoglycan link protein 1 (Hapln1), hemoglobin beta-2 subunit, type I procollagen (Col1a2), retinoblastoma binding protein 4 (LOC685491), Sparc-related modular calcium binding 2 (Smoc2), and calpastatin (Cast). Other genes were highly expressed in cells from both PC and RZ zones, including collagen II, collagen IX, catenin (cadherin associated protein) beta 1, eukaryotic translation elongation factor, high mobility group, ribosomal protein, microtubule-associated protein, reticulocalbin, thrombospondin, retinoblastoma binding protein, carboxypeptidase E, carnitine palmitoyltransferase 1, cysteine rich glycoprotein, plexin B2 (Plxnb2), and gap junction membrane channel protein. Functional classification of the most highly expressed transcripts were analyzed, and the pathway analysis indicated that ossification, bone remodeling, and cartilage development were uniquely enriched in the PC whereas both the PC and RZ showed pathway enrichment for skeletal development, extracellular matrix structural constituent, proteinaceous extracellular matrix, collagen, extracellular matrix, and extracellular matrix part pathways. We conclude that differential gene expression exists between the RZ and PC chondrocytes and these differentially expressed genes have unique roles to play corresponding to the function of their respective zones. PMID:18579462

  8. Probing the coagulation pathway with aptamers identifies combinations that synergistically inhibit blood clot formation.

    PubMed

    Bompiani, Kristin M; Lohrmann, Jens L; Pitoc, George A; Frederiksen, James W; Mackensen, George B; Sullenger, Bruce A

    2014-08-14

    Coordinated enzymatic reactions regulate blood clot generation. To explore the contributions of various coagulation enzymes in this process, we utilized a panel of aptamers against factors VIIa, IXa, Xa, and prothrombin. Each aptamer dose-dependently inhibited clot formation, yet none was able to completely impede this process in highly procoagulant settings. However, several combinations of two aptamers synergistically impaired clot formation. One extremely potent aptamer combination was able to maintain human blood fluidity even during extracorporeal circulation, a highly procoagulant setting encountered during cardiopulmonary bypass surgery. Moreover, this aptamer cocktail could be rapidly reversed with antidotes to restore normal hemostasis, indicating that even highly potent aptamer combinations can be rapidly controlled. These studies highlight the potential utility of using sets of aptamers to probe the functions of proteins in molecular pathways for research and therapeutic ends. PMID:25065530

  9. Non-host disease resistance response in pea (Pisum sativum) pods: Biochemical function of DRR206 and phytoalexin pathway localization.

    PubMed

    Seneviratne, Herana Kamal; Dalisay, Doralyn S; Kim, Kye-Won; Moinuddin, Syed G A; Yang, Hong; Hartshorn, Christopher M; Davin, Laurence B; Lewis, Norman G

    2015-05-01

    Continually exposed to potential pathogens, vascular plants have evolved intricate defense mechanisms to recognize encroaching threats and defend themselves. They do so by inducing a set of defense responses that can help defeat and/or limit effects of invading pathogens, of which the non-host disease resistance response is the most common. In this regard, pea (Pisum sativum) pod tissue, when exposed to Fusarium solani f. sp. phaseoli spores, undergoes an inducible transcriptional activation of pathogenesis-related genes, and also produces (+)-pisatin, its major phytoalexin. One of the inducible pathogenesis-related genes is Disease Resistance Response-206 (DRR206), whose role in vivo was unknown. DRR206 is, however, related to the dirigent protein (DP) family. In this study, its biochemical function was investigated in planta, with the metabolite associated with its gene induction being pinoresinol monoglucoside. Interestingly, both pinoresinol monoglucoside and (+)-pisatin were co-localized in pea pod endocarp epidermal cells, as demonstrated using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging. In addition, endocarp epidermal cells are also the site for both chalcone synthase and DRR206 gene expression. Taken together, these data indicate that both (+)-pisatin and pinoresinol monoglucoside function in the overall phytoalexin responses. PMID:25457488

  10. Transport of dissolved organic carbon from soil to surface water: Identifying the transport pathways

    NASA Astrophysics Data System (ADS)

    Van Gaelen, Nele

    2013-04-01

    Over the last decades, increasing concentrations of dissolved organic carbon (DOC) have been found in surface waters. It has also become clear that land use is an important driver for DOC export. However, causal factors controlling this temporal and spatial variation are not clear. Efforts to model DOC export on a catchment scale are rare. In this research, we aim to determine the factors controlling variations in DOC concentration and quality in surface waters. Secondly, the importance of the different pathways (surface runoff, subsurface flow and groundwater flow) for the transport of dissolved organic matter from the soil to the surface water is investigated. Six headwater catchments (100 - 400 ha) were selected in Belgium, representing three different types of land use, namely forest, grassland and arable land. At the outlet of each catchment, a flow-proportional sampler has been collecting samples of base flow and peak discharge since January 2010. In addition, samples of groundwater, subsurface water and precipitation water were collected on a regular base in three of the catchments. Samples were analyzed for DOC, specific UV absorbance (SUVA) and dissolved silica (DSi). Elemental analysis was carried out using ICP-OES. Since 2012, precipitation water and a selection of river water samples was also analyzed for O and H isotopes. Overall, DOC concentrations were highest in forest catchments and lowest in grassland catchments. For all land use types, measured DOC concentrations were highest during peak discharge. The rise in DOC concentrations was associated with a change in DOC quality. During periods of greater discharge, higher SUVA values were measured, indicating DOC with higher aromaticity (humic and fulvic fractions) reaches the outlet. ICP and DSi results also showed a significant difference in geochemical composition of the river water if peak events are compared to base flow samples. During an event, Ca, Mg, Na, S and DSi concentrations were lowered, while K concentrations rose. Isotope analysis showed more heavy O an H isotopes during peak events than during baseflow. Results of the river water were combined with analysis of possible end-members in the catchments, using the groundwater, soil water and precipitation samples. An end-member-mixing-analysis (EMMA) gained more insight into the contributing pathways for the transport of organic matter from the soil to the surface water during base and peak flow. Furthermore, results from the different catchments were compared, and allowed to relate DOC transport to land use type. This is an important step towards a model describing DOC transport at the catchment scale.

  11. Systematic mapping of genetic interactions in Caenorhabditis elegans identifies common modifiers of diverse signaling pathways

    Microsoft Academic Search

    Ben Lehner; Catriona Crombie; Julia Tischler; Angelo Fortunato; Andrew G Fraser

    2006-01-01

    Most heritable traits, including disease susceptibility, are affected by interactions between multiple genes. However, we understand little about how genes interact because very few possible genetic interactions have been explored experimentally. We have used RNA interference in Caenorhabditis elegans to systematically test ?65,000 pairs of genes for their ability to interact genetically. We identify ?350 genetic interactions between genes functioning

  12. Identifiable Achatina giant neurones: Their localizations in ganglia, axonal pathways and pharmacological features

    Microsoft Academic Search

    Hiroshi Takeuchi; Yoko Araki; Muhammad Emaduddin; Wei Zhang; Xiao Yan Han; Thucydides L. Salunga; Shu Min Wong

    1996-01-01

    1.1. An African giant snail (Achatina fulica Férussac), originally from East Africa, is now found abundantly in tropical and subtropical regions of Asia, including Okinawa in Japan. This is one of the largest land snail species in the world. The Achatina central nervous system is composed of the buccal, cerebral and suboesophageal ganglia. The 37 giant neurones were identified in

  13. Biochemical characterization of recombinant ?-carbonic anhydrase (PgiCAb) identified in the genome of the oral pathogenic bacterium Porphyromonas gingivalis.

    PubMed

    Del Prete, Sonia; Vullo, Daniela; De Luca, Viviana; AlOthman, Zeid; Osman, Sameh M; Supuran, Claudiu T; Capasso, Clemente

    2015-06-01

    Carbonic anhydrases (CAs, EC 4.2.1.1) belonging to the ?-, ?-, ?-, ?- and ?-CAs are ubiquitous metalloenzymes present in prokaryotes and eukaryotes. CAs started to be investigated in detail only recently in pathogenic bacteria, in the search for antibiotics with a novel mechanism of action, since it has been demonstrated that in many such organisms they are essential for the life cycle of the organism. CA inhibition leads to growth impairment or growth defects in several pathogenic bacteria. The microbiota of the human oral mucosa consists of a myriad of bacterial species, Porphyromonas gingivalis being one of them and the major pathogen responsible for the development of chronic periodontitis. The genome of P. gingivalis encodes for a ?- and a ?-CAs. Recently, our group purified the recombinant ?-CA (named PgiCA) which was shown to possess a significant catalytic activity for the reaction that converts CO2 to bicarbonate and protons, with a kcat of 4.1?×?10(5?)s(-1) and a kcat/Km of 5.4?×?10(7?)M(-1?)×?s(-1). We have also investigated its inhibition profile with a range of inorganic anions such as thiocyanate, cyanide, azide, hydrogen sulfide, sulfamate and trithiocarbonate. Here, we describe the cloning, purification and kinetic parameters of the other class of CA identified in the genome of P. gingivalis, the ?-CA, named PgiCAb. This enzyme has a good catalytic activity, with a kcat of 2.8?×?10(5?)s(-1) and a kcat/Km of 1.5?×?10(7?)M(-1?)×?s(-1). PgiCAb was also inhibited by the clinically used sulfonamide acetazolamide, with an inhibition constant of 214?nM. The role of CAs as possible virulence factors of P. gingivalis is poorly understood at the moment but their good catalytic activity and the fact that they might be inhibited by a large number of compounds, which may pave the way for finding inhibitors with antibacterial activity that may elucidate these phenomena and lead to novel antibiotics. PMID:25032746

  14. RNAi screen identifies a role for adaptor protein AP-3 in sorting to the regulated secretory pathway

    PubMed Central

    Asensio, Cédric S.; Sirkis, Daniel W.

    2010-01-01

    The regulated release of proteins depends on their inclusion within large dense-core vesicles (LDCVs) capable of regulated exocytosis. LDCVs form at the trans-Golgi network (TGN), but the mechanism for protein sorting to this regulated secretory pathway (RSP) and the cytosolic machinery involved in this process have remained poorly understood. Using an RNA interference screen in Drosophila melanogaster S2 cells, we now identify a small number of genes, including several subunits of the heterotetrameric adaptor protein AP-3, which are required for sorting to the RSP. In mammalian neuroendocrine cells, loss of AP-3 dysregulates exocytosis due to a primary defect in LDCV formation. Previous work implicated AP-3 in the endocytic pathway, but we find that AP-3 promotes sorting to the RSP within the biosynthetic pathway at the level of the TGN. Although vesicles with a dense core still form in the absence of AP-3, they contain substantially less synaptotagmin 1, indicating that AP-3 concentrates the proteins required for regulated exocytosis. PMID:21149569

  15. A systems biology approach to identify intelligence quotient score-related genomic regions, and pathways relevant to potential therapeutic treatments

    PubMed Central

    Zhao, Min; Kong, Lei; Qu, Hong

    2014-01-01

    Although the intelligence quotient (IQ) is the most popular intelligence test in the world, little is known about the underlying biological mechanisms that lead to the differences in human. To improve our understanding of cognitive processes and identify potential biomarkers, we conducted a comprehensive investigation of 158 IQ-related genes selected from the literature. A genomic distribution analysis demonstrated that IQ-related genes were enriched in seven regions of chromosome 7 and the X chromosome. In addition, these genes were enriched in target lists of seven transcription factors and sixteen microRNAs. Using a network-based approach, we further reconstructed an IQ-related pathway from known human pathway interaction data. Based on this reconstructed pathway, we incorporated enriched drugs and described the importance of dopamine and norepinephrine systems in IQ-related biological process. These findings not only reveal several testable genes and processes related to IQ scores, but also have potential therapeutic implications for IQ-related mental disorders. PMID:24566931

  16. Oxygen and Hydrogen Peroxide in the Early Evolution of Life on Earth: In silico Comparative Analysis of Biochemical Pathways

    PubMed Central

    ?lesak, Halina; Kruk, Jerzy

    2012-01-01

    Abstract In the Universe, oxygen is the third most widespread element, while on Earth it is the most abundant one. Moreover, oxygen is a major constituent of all biopolymers fundamental to living organisms. Besides O2, reactive oxygen species (ROS), among them hydrogen peroxide (H2O2), are also important reactants in the present aerobic metabolism. According to a widely accepted hypothesis, aerobic metabolism and many other reactions/pathways involving O2 appeared after the evolution of oxygenic photosynthesis. In this study, the hypothesis was formulated that the Last Universal Common Ancestor (LUCA) was at least able to tolerate O2 and detoxify ROS in a primordial environment. A comparative analysis was carried out of a number of the O2-and H2O2-involving metabolic reactions that occur in strict anaerobes, facultative anaerobes, and aerobes. The results indicate that the most likely LUCA possessed O2-and H2O2-involving pathways, mainly reactions to remove ROS, and had, at least in part, the components of aerobic respiration. Based on this, the presence of a low, but significant, quantity of H2O2 and O2 should be taken into account in theoretical models of the early Archean atmosphere and oceans and the evolution of life. It is suggested that the early metabolism involving O2/H2O2 was a key adaptation of LUCA to already existing weakly oxic zones in Earth's primordial environment. Key Words: Hydrogen peroxide—Oxygen—Origin of life—Photosynthesis—Superoxide dismutase—Superoxide reductase. Astrobiology 12, 775–784. PMID:22970865

  17. Perceived discrimination as a stressor for close relationships: identifying psychological and physiological pathways.

    PubMed

    Doyle, David Matthew; Molix, Lisa

    2014-12-01

    Approaching the inverse association between perceived discrimination and close relationship functioning from a stress and coping framework, we propose and test a novel model incorporating psychological (emotion dysregulation) and physiological (chronic inflammation) pathways. Analyses of data from a sample of African American participants (N = 592) enrolled in the Midlife in the United States (MIDUS) study revealed support for the proposed model. Specifically, results from structural equation modeling analyses showed that perceived discrimination was indirectly associated with increased emotion dysregulation (venting and denial) through stressor appraisals and directly associated with increased inflammation (interluekin-6, e-selectin and c-reactive protein). Furthermore, relationship strain with family, friends and spouses was associated with greater levels of emotion dysregulation and chronic inflammation. Overall, the proposed model fit the data well and provides support for new avenues of research on the social, psychological and physiological correlates of perceived discrimination and close relationship functioning. To conclude, evidence for the proposed biopsychosocial model is summarized and directions for future research on these topics are discussed. PMID:24659156

  18. Novel pancreatic endocrine maturation pathways identified by genomic profiling and causal reasoning.

    PubMed

    Gutteridge, Alex; Rukstalis, J Michael; Ziemek, Daniel; Tié, Mark; Ji, Lin; Ramos-Zayas, Rebeca; Nardone, Nancy A; Norquay, Lisa D; Brenner, Martin B; Tang, Kim; McNeish, John D; Rowntree, Rebecca K

    2013-01-01

    We have used a previously unavailable model of pancreatic development, derived in vitro from human embryonic stem cells, to capture a time-course of gene, miRNA and histone modification levels in pancreatic endocrine cells. We investigated whether it is possible to better understand, and hence control, the biological pathways leading to pancreatic endocrine formation by analysing this information and combining it with the available scientific literature to generate models using a casual reasoning approach. We show that the embryonic stem cell differentiation protocol is highly reproducible in producing endocrine precursor cells and generates cells that recapitulate many aspects of human embryonic pancreas development, including maturation into functional endocrine cells when transplanted into recipient animals. The availability of whole genome gene and miRNA expression data from the early stages of human pancreatic development will be of great benefit to those in the fields of developmental biology and diabetes research. Our causal reasoning algorithm suggested the involvement of novel gene networks, such as NEUROG3/E2F1/KDM5B and SOCS3/STAT3/IL-6, in endocrine cell development We experimentally investigated the role of the top-ranked prediction by showing that addition of exogenous IL-6 could affect the expression of the endocrine progenitor genes NEUROG3 and NKX2.2. PMID:23418498

  19. Ectopic Pregnancy as a Model to Identify Endometrial Genes and Signaling Pathways Important in Decidualization and Regulated by Local Trophoblast

    PubMed Central

    Burgess, Stewart; McDonald, Sarah E.; Critchley, Hilary O. D.; Horne, Andrew W.

    2011-01-01

    The endometrium in early pregnancy undergoes decidualization and functional changes induced by local trophoblast, which are not fully understood. We hypothesized that endometrium from tubal ectopic pregnancy (EP) could be interrogated to identify novel genes and pathways involved in these processes. Gestation-matched endometrium was collected from women with EP (n?=?11) and intrauterine pregnancies (IUP) (n?=?13). RNA was extracted from the tissue. In addition, tissues were prepared for histological analysis for degree of decidualization. We compared a) the samples from EP that were decidualized (n?=?6) with non-decidualized samples (n?=?5), and b) the decidualized EP (n?=?6) with decidualization-matched IUP (n?=?6) samples using an Affymetrix gene array platform, with Ingenuity Pathway Analysis, combined with quantitative RT-PCR. Expression of PRL and IGFBP1 was used to confirm the degree of decidualization in each group. There were no differences in PRL or IGFBP1 expression in the decidualization-matched samples but a marked reduction (P<0.001) in the non-decidualized samples. Decidualization was associated with increased expression of 428 genes including SCARA5 (181-fold), DKK1 (71-fold) and PROK1 (32-fold), and decreased expression of 230 genes including MMP-7 (35-fold) and SFRP4 (21-fold). The top canonical pathways associated with these differentially expressed genes were Natural Killer Cell and Wnt/b-Catenin signaling. Local trophoblast was associated with much less alteration of endometrial gene expression with an increase in 56 genes, including CSH1 (8-fold), and a reduction in 29 genes including CRISP3 (8-fold). The top associated canonical pathway was Antigen Presentation. The study of endometrium from tubal EP may promote novel insights into genes involved in decidualization and those influenced by factors from neighboring trophoblast. This has afforded unique information not highlighted by previous studies and adds to our understanding of the endometrium in early pregnancy. PMID:21858178

  20. Identifying vulnerable pathways in Mycobacterium tuberculosis by using a knockdown approach.

    PubMed

    Carroll, Paul; Faray-Kele, Marie-Claire; Parish, Tanya

    2011-07-01

    We constructed recombinant strains of Mycobacterium tuberculosis in which expression of specific genes was downregulated to identify vulnerable drug targets. Growth phenotypes in macrophages and culture were used to rank targets: the dprE1, clpP1, and fadD32 operons were the best targets and glnA1, glnE, pknL, regX3, and senX3 were poor targets. PMID:21642404

  1. Cell-Based Assay To Identify Inhibitors of the Hfq-sRNA Regulatory Pathway

    PubMed Central

    El-Mowafi, Shaima A.; Alumasa, John N.; Ades, Sarah E.

    2014-01-01

    Noncoding small RNAs (sRNAs) act in conjunction with the RNA chaperone Hfq to regulate gene expression in bacteria. Because Hfq is required for virulence in several bacterial pathogens, the Hfq-sRNA system is an attractive target for antibiotic development. A reporter strain in which the expression of yellow fluorescent protein (YFP) is controlled by Hfq-sRNA was engineered to identify inhibitors of this system. A reporter that is targeted by Hfq in conjunction with the RybB sRNA was used in a genetic screen to identify inhibitors from a library of cyclic peptides produced in Escherichia coli using split-intein circular ligation of peptides and proteins (SICLOPPS), an intein-based technology. One cyclic peptide identified in this screen, RI20, inhibited Hfq-mediated repression of gene expression in conjunction with both RybB and an unrelated sRNA, MicF. Gel mobility shift assays showed that RI20 inhibited binding of Hfq to RybB and MicF with similar Ki values. These data suggest that RI20 inhibits Hfq activity by blocking interactions with sRNAs and provide a paradigm for inhibiting virulence genes in Gram-negative pathogens. PMID:25001303

  2. Forward genetic screen for malignant peripheral nerve sheath tumor formation identifies new genes and pathways driving tumorigenesis.

    PubMed

    Rahrmann, Eric P; Watson, Adrienne L; Keng, Vincent W; Choi, Kwangmin; Moriarity, Branden S; Beckmann, Dominic A; Wolf, Natalie K; Sarver, Aaron; Collins, Margaret H; Moertel, Christopher L; Wallace, Margaret R; Gel, Bernat; Serra, Eduard; Ratner, Nancy; Largaespada, David A

    2013-07-01

    Malignant peripheral nerve sheath tumors (MPNSTs) are sarcomas of Schwann cell lineage origin that occur sporadically or in association with the inherited syndrome neurofibromatosis type 1. To identify genetic drivers of MPNST development, we used the Sleeping Beauty (SB) transposon-based somatic mutagenesis system in mice with somatic loss of transformation-related protein p53 (Trp53) function and/or overexpression of human epidermal growth factor receptor (EGFR). Common insertion site (CIS) analysis of 269 neurofibromas and 106 MPNSTs identified 695 and 87 sites with a statistically significant number of recurrent transposon insertions, respectively. Comparison to human data sets identified new and known driver genes for MPNST formation at these sites. Pairwise co-occurrence analysis of CIS-associated genes identified many cooperating mutations that are enriched in Wnt/?-catenin, PI3K-AKT-mTOR and growth factor receptor signaling pathways. Lastly, we identified several new proto-oncogenes, including Foxr2 (encoding forkhead box R2), which we functionally validated as a proto-oncogene involved in MPNST maintenance. PMID:23685747

  3. Temporal expression profiling identifies pathways mediating effect of causal variant on phenotype.

    PubMed

    Gupta, Saumya; Radhakrishnan, Aparna; Raharja-Liu, Pandu; Lin, Gen; Steinmetz, Lars M; Gagneur, Julien; Sinha, Himanshu

    2015-06-01

    Even with identification of multiple causal genetic variants for common human diseases, understanding the molecular processes mediating the causal variants' effect on the disease remains a challenge. This understanding is crucial for the development of therapeutic strategies to prevent and treat disease. While static profiling of gene expression is primarily used to get insights into the biological bases of diseases, it makes differentiating the causative from the correlative effects difficult, as the dynamics of the underlying biological processes are not monitored. Using yeast as a model, we studied genome-wide gene expression dynamics in the presence of a causal variant as the sole genetic determinant, and performed allele-specific functional validation to delineate the causal effects of the genetic variant on the phenotype. Here, we characterized the precise genetic effects of a functional MKT1 allelic variant in sporulation efficiency variation. A mathematical model describing meiotic landmark events and conditional activation of MKT1 expression during sporulation specified an early meiotic role of this variant. By analyzing the early meiotic genome-wide transcriptional response, we demonstrate an MKT1-dependent role of novel modulators, namely, RTG1/3, regulators of mitochondrial retrograde signaling, and DAL82, regulator of nitrogen starvation, in additively effecting sporulation efficiency. In the presence of functional MKT1 allele, better respiration during early sporulation was observed, which was dependent on the mitochondrial retrograde regulator, RTG3. Furthermore, our approach showed that MKT1 contributes to sporulation independent of Puf3, an RNA-binding protein that steady-state transcription profiling studies have suggested to mediate MKT1-pleiotropic effects during mitotic growth. These results uncover interesting regulatory links between meiosis and mitochondrial retrograde signaling. In this study, we highlight the advantage of analyzing allele-specific transcriptional dynamics of mediating genes. Applications in higher eukaryotes can be valuable for inferring causal molecular pathways underlying complex dynamic processes, such as development, physiology and disease progression. PMID:26039065

  4. Abiogenic hydrocarbon isotopic signatures in granitic rocks: Identifying pathways of formation

    NASA Astrophysics Data System (ADS)

    Potter, Joanna; Salvi, Stefano; Longstaffe, Fred J.

    2013-12-01

    The stability and isotopic composition of hydrocarbons formed in the mantle are controversial subjects. Knowing the range in isotopic compositions of abiogenically-derived hydrocarbons is important for recognising biological signatures in ancient and extra-terrestrial materials. In an effort to enhance this database, stable isotope results are reported here for hydrocarbon-bearing fluid inclusions hosted in two peralkaline igneous complexes from Lovozero, Russia and Strange Lake, Canada. Based on the distribution of isotopic compositions, we propose three pathways for abiogenically-generated hydrocarbons. Type-1 (?13CCH4 > ?13CCO2 and ?13CC2 +) represents mantle-derived hydrocarbons generated in equilibrium with hyperagpaitic magmas in the upper mantle, and suggests that mantle CH4 and C2H6?13C and ?2H could have values of ~ - 5.3 and ~ - 112‰, and ~ - 10.8 and - 162‰, respectively. Type-2 (?13CCO2 > ?13CCH4 > ?13CC2 +) represents Fischer-Tropsch-type hydrocarbon generation in quartz-bearing peralkaline rocks with CO2 as the initial magmatic gas phase. For Type-2, ?13CCO2 values are ~ - 2‰, whereas ?13CCH4 and ?2HCH4 values range from - 32 to - 20‰ and - 170 and - 160‰, respectively. The ?13CC2H6 values are slightly lower than associated ?13CCH4 values. Type-3 (?13CCO2 > ?13CCH4 < ?13CC2 +) represents an overprint of Type-2, formed during low temperature alteration of quartz-bearing peralkaline rocks. Here, ?13CCO2 values are variable, - 14.0 to - 9.5‰, ?13CCH4 values range from - 30.8 to - 20.8‰ while ?13CC2H6 values are higher than associated ?13CCH4 values. Both Type-2 and Type-3 isotopic compositions mimic patterns normally considered to be thermogenic in origin, thus demonstrating that isotopic data alone cannot be used reliably to distinguish between hydrocarbons of abiogenic versus biogenic origin.

  5. Temporal Expression Profiling Identifies Pathways Mediating Effect of Causal Variant on Phenotype

    PubMed Central

    Gupta, Saumya; Radhakrishnan, Aparna; Raharja-Liu, Pandu; Lin, Gen; Steinmetz, Lars M.; Gagneur, Julien; Sinha, Himanshu

    2015-01-01

    Even with identification of multiple causal genetic variants for common human diseases, understanding the molecular processes mediating the causal variants’ effect on the disease remains a challenge. This understanding is crucial for the development of therapeutic strategies to prevent and treat disease. While static profiling of gene expression is primarily used to get insights into the biological bases of diseases, it makes differentiating the causative from the correlative effects difficult, as the dynamics of the underlying biological processes are not monitored. Using yeast as a model, we studied genome-wide gene expression dynamics in the presence of a causal variant as the sole genetic determinant, and performed allele-specific functional validation to delineate the causal effects of the genetic variant on the phenotype. Here, we characterized the precise genetic effects of a functional MKT1 allelic variant in sporulation efficiency variation. A mathematical model describing meiotic landmark events and conditional activation of MKT1 expression during sporulation specified an early meiotic role of this variant. By analyzing the early meiotic genome-wide transcriptional response, we demonstrate an MKT1-dependent role of novel modulators, namely, RTG1/3, regulators of mitochondrial retrograde signaling, and DAL82, regulator of nitrogen starvation, in additively effecting sporulation efficiency. In the presence of functional MKT1 allele, better respiration during early sporulation was observed, which was dependent on the mitochondrial retrograde regulator, RTG3. Furthermore, our approach showed that MKT1 contributes to sporulation independent of Puf3, an RNA-binding protein that steady-state transcription profiling studies have suggested to mediate MKT1-pleiotropic effects during mitotic growth. These results uncover interesting regulatory links between meiosis and mitochondrial retrograde signaling. In this study, we highlight the advantage of analyzing allele-specific transcriptional dynamics of mediating genes. Applications in higher eukaryotes can be valuable for inferring causal molecular pathways underlying complex dynamic processes, such as development, physiology and disease progression. PMID:26039065

  6. Label-free quantitative urinary proteomics identifies the arginase pathway as a new player in congenital obstructive nephropathy.

    PubMed

    Lacroix, Chrystelle; Caubet, Cécile; Gonzalez-de-Peredo, Anne; Breuil, Benjamin; Bouyssié, David; Stella, Alexandre; Garrigues, Luc; Le Gall, Caroline; Raevel, Anthony; Massoubre, Angelique; Klein, Julie; Decramer, Stéphane; Sabourdy, Frédérique; Bandin, Flavio; Burlet-Schiltz, Odile; Monsarrat, Bernard; Schanstra, Joost-Peter; Bascands, Jean-Loup

    2014-12-01

    Obstructive nephropathy is a frequently encountered situation in newborns. In previous studies, the urinary peptidome has been analyzed for the identification of clinically useful biomarkers of obstructive nephropathy. However, the urinary proteome has not been explored yet and should allow additional insight into the pathophysiology of the disease. We have analyzed the urinary proteome of newborns (n = 5/group) with obstructive nephropathy using label free quantitative nanoLC-MS/MS allowing the identification and quantification of 970 urinary proteins. We next focused on proteins exclusively regulated in severe obstructive nephropathy and identified Arginase 1 as a potential candidate molecule involved in the development of obstructive nephropathy, located at the crossroad of pro- and antifibrotic pathways. The reduced urinary abundance of Arginase 1 in obstructive nephropathy was verified in independent clinical samples using both Western blot and MRM analysis. These data were confirmed in situ in kidneys obtained from a mouse obstructive nephropathy model. In addition, we also observed increased expression of Arginase 2 and increased total arginase activity in obstructed mouse kidneys. mRNA expression analysis of the related arginase pathways indicated that the pro-fibrotic arginase-related pathway is activated during obstructive nephropathy. Taken together we have identified a new actor in the development of obstructive nephropathy in newborns using quantitative urinary proteomics and shown its involvement in an in vivo model of disease. The present study demonstrates the relevance of such a quantitative urinary proteomics approach with clinical samples for a better understanding of the pathophysiology and for the discovery of potential therapeutic targets. PMID:25205225

  7. Novel MEK1 Mutation Identified by Mutational Analysis of Epidermal Growth Factor Receptor Signaling Pathway Genes in Lung Adenocarcinoma

    PubMed Central

    Marks, Jenifer L.; Gong, Yixuan; Chitale, Dhananjay; Golas, Ben; McLellan, Michael D.; Kasai, Yumi; Ding, Li; Mardis, Elaine R.; Wilson, Richard K.; Solit, David; Levine, Ross; Michel, Kathrin; Thomas, Roman K.; Rusch, Valerie W.; Ladanyi, Marc; Pao, William

    2008-01-01

    Genetic lesions affecting a number of kinases and other elements within the epidermal growth factor receptor (EGFR) signaling pathway have been implicated in the pathogenesis of human non–small-cell lung cancer (NSCLC). We performed mutational profiling of a large cohort of lung adenocarcinomas to uncover other potential somatic mutations in genes of this pathway that could contribute to lung tumorigenesis. We have identified in 2 of 207 primary lung tumors a somatic activating mutation in exon 2 of MEK1 (i.e., mitogen-activated protein kinase kinase 1 or MAP2K1) that substitutes asparagine for lysine at amino acid 57 (K57N) in the nonkinase portion of the kinase. Neither of these two tumors harbored known mutations in other genes encoding components of the EGFR signaling pathway (i.e., EGFR, HER2, KRAS, PIK3CA, and BRAF). Expression of mutant, but not wild-type, MEK1 leads to constitutive activity of extracellular signal–regulated kinase (ERK)-1/2 in human 293T cells and to growth factor–independent proliferation of murine Ba/F3 cells. A selective MEK inhibitor, AZD6244, inhibits mutant-induced ERK activity in 293T cells and growth of mutant-bearing Ba/F3 cells. We also screened 85 NSCLC cell lines for MEK1 exon 2 mutations; one line (NCI-H1437) harbors a Q56P substitution, a known transformation-competent allele of MEK1 originally identified in rat fibroblasts, and is sensitive to treatment with AZD6244. MEK1 mutants have not previously been reported in lung cancer and may provide a target for effective therapy in a small subset of patients with lung adenocarcinoma. PMID:18632602

  8. Enhanced Sequential Search Methodology for Identifying Cost-Optimal Building Pathways

    SciTech Connect

    Horowitz, S.; Christensen, C.; Brandemuehl, M.; Krarti, M.

    2008-06-01

    The BEopt software is a building energy optimization tool that generates a cost-optimal path of building designs from a reference building up to zero-net energy. It employs a sequential search methodology to account for complex energy interactions between building efficiency measures. Enhancement strategies to this search methodology are developed to increase accuracy (ability to identify the true cost-optimal curve) and speed (number of required energy simulations). A test suite of optimizations is used to gauge the effectiveness of each strategy. Combinations of strategies are assembled into packages, ranging from conservative to aggressive, with so up to 71% fewer required simulations are required.

  9. Molecular and Biochemical Characterization of the 5-Nitroanthranilic Acid Degradation Pathway in Bradyrhizobium sp. Strain JS329 ? †

    PubMed Central

    Qu, Yi; Spain, Jim C.

    2011-01-01

    Biodegradation pathways of synthetic nitroaromatic compounds and anilines are well documented, but little is known about those of nitroanilines. We previously reported that the initial step in 5-nitroanthranilic acid (5NAA) degradation by Bradyrhizobium sp. strain JS329 is a hydrolytic deamination to form 5-nitrosalicylic acid (5NSA), followed by ring fission catalyzed by 5NSA dioxygenase. The mechanism of release of the nitro group was unknown. In this study, we subcloned, sequenced, and expressed the genes encoding 5NAA deaminase (5NAA aminohydrolase, NaaA), 5NSA dioxygenase (NaaB) and lactonase (NaaC), the key genes responsible for 5NAA degradation. Sequence analysis and enzyme characterization revealed that NaaA is a hydrolytic metalloenzyme with a narrow substrate range. The nitro group is spontaneously eliminated as nitrite concomitant with the formation of a lactone from the ring fission product of 5NSA dioxygenation. The elimination of the nitro group during lactone formation is a previously unreported mechanism for denitration of nitro aliphatic compounds. PMID:21498645

  10. Biochemical and genetic interaction between the fragile X mental retardation protein and the microRNA pathway

    Microsoft Academic Search

    Peng Jin; Daniela C Zarnescu; Stephanie Ceman; Mika Nakamoto; Julie Mowrey; Thomas A Jongens; David L Nelson; Kevin Moses; Stephen T Warren

    2004-01-01

    Fragile X syndrome is caused by a loss of expression of the fragile X mental retardation protein (FMRP). FMRP is a selective RNA-binding protein which forms a messenger ribonucleoprotein (mRNP) complex that associates with polyribosomes. Recently, mRNA ligands associated with FMRP have been identified. However, the mechanism by which FMRP regulates the translation of its mRNA ligands remains unclear. MicroRNAs

  11. Evolution of a Pathogen: A Comparative Genomics Analysis Identifies a Genetic Pathway to Pathogenesis in Acinetobacter

    PubMed Central

    Sahl, Jason W.; Gillece, John D.; Schupp, James M.; Waddell, Victor G.; Driebe, Elizabeth M.; Engelthaler, David M.; Keim, Paul

    2013-01-01

    Acinetobacter baumannii is an emergent and global nosocomial pathogen. In addition to A. baumannii, other Acinetobacter species, especially those in the Acinetobacter calcoaceticus-baumannii (Acb) complex, have also been associated with serious human infection. Although mechanisms of attachment, persistence on abiotic surfaces, and pathogenesis in A. baumannii have been identified, the genetic mechanisms that explain the emergence of A. baumannii as the most widespread and virulent Acinetobacter species are not fully understood. Recent whole genome sequencing has provided insight into the phylogenetic structure of the genus Acinetobacter. However, a global comparison of genomic features between Acinetobacter spp. has not been described in the literature. In this study, 136 Acinetobacter genomes, including 67 sequenced in this study, were compared to identify the acquisition and loss of genes in the expansion of the Acinetobacter genus. A whole genome phylogeny confirmed that A. baumannii is a monophyletic clade and that the larger Acb complex is also a well-supported monophyletic group. The whole genome phylogeny provided the framework for a global genomic comparison based on a blast score ratio (BSR) analysis. The BSR analysis demonstrated that specific genes have been both lost and acquired in the evolution of A. baumannii. In addition, several genes associated with A. baumannii pathogenesis were found to be more conserved in the Acb complex, and especially in A. baumannii, than in other Acinetobacter genomes; until recently, a global analysis of the distribution and conservation of virulence factors across the genus was not possible. The results demonstrate that the acquisition of specific virulence factors has likely contributed to the widespread persistence and virulence of A. baumannii. The identification of novel features associated with transcriptional regulation and acquired by clades in the Acb complex presents targets for better understanding the evolution of pathogenesis and virulence in the expansion of the genus. PMID:23365658

  12. Exploring critical pathways for urban water management to identify robust strategies under deep uncertainties.

    PubMed

    Urich, Christian; Rauch, Wolfgang

    2014-12-01

    Long-term projections for key drivers needed in urban water infrastructure planning such as climate change, population growth, and socio-economic changes are deeply uncertain. Traditional planning approaches heavily rely on these projections, which, if a projection stays unfulfilled, can lead to problematic infrastructure decisions causing high operational costs and/or lock-in effects. New approaches based on exploratory modelling take a fundamentally different view. Aim of these is, to identify an adaptation strategy that performs well under many future scenarios, instead of optimising a strategy for a handful. However, a modelling tool to support strategic planning to test the implication of adaptation strategies under deeply uncertain conditions for urban water management does not exist yet. This paper presents a first step towards a new generation of such strategic planning tools, by combing innovative modelling tools, which coevolve the urban environment and urban water infrastructure under many different future scenarios, with robust decision making. The developed approach is applied to the city of Innsbruck, Austria, which is spatially explicitly evolved 20 years into the future under 1000 scenarios to test the robustness of different adaptation strategies. Key findings of this paper show that: (1) Such an approach can be used to successfully identify parameter ranges of key drivers in which a desired performance criterion is not fulfilled, which is an important indicator for the robustness of an adaptation strategy; and (2) Analysis of the rich dataset gives new insights into the adaptive responses of agents to key drivers in the urban system by modifying a strategy. PMID:25240118

  13. Using End-Member Mixing Analysis to Identify Transport Pathways in Agricultural Watersheds

    NASA Astrophysics Data System (ADS)

    Essaid, H.

    2013-12-01

    Concentrations of naturally occurring solutes were monitored in six agricultural watersheds as part of the Agricultural Chemical Sources, Transport and Fate study of the U.S. Geological Survey National Water Quality Assessment Program. The watersheds, located in Indiana (IN), Iowa (IA), Maryland (MD), Nebraska (NE), Mississippi (MS) and Washington (WA), ranged in size from 5 to 1300 square kilometers, and agricultural land use accounted for 60 - 98% of the watershed area. Concentrations of chloride, calcium, magnesium, sodium, potassium, fluoride, sulfate and silica in stream water were analyzed using principal components analysis (PCA) to identify the dominant processes controlling stream water chemistry. Concentrations measured in wells, streambed piezometers, unsaturated zone lysimeters, overland flow, and tile drains were then used to project the chemistry of these flow compartments/components onto the stream chemistry PCA transformation. This facilitated the identification of end members explaining observed stream chemistry, and the source of the water for these end members. The majority of the variance in stream chemistry could be explained by the mixing of three end-members: 94% for Leary Weber Ditch, IN; 84% for South Fork Iowa River, IA; 91% for Morgan Creek, MD; 81% for Maple Creek, NE; 92% for Tommie Bayou, MS; and, 97% for DR2, WA. The chemistry of overland flow and tile drainage was also contained within the end member concentrations. The end members were generally represented by two groundwater components and a very low solute concentration component (precipitation or irrigation water) that diluted the groundwater signal. Generally, one groundwater component represented recently recharged water that resembled the concentration of water in the deepest unsaturated zone lysimeters, and the other groundwater component was representative of regional groundwater conditions. Compared to regional groundwater, the recent groundwater component had lower concentrations of solutes derived from rock weathering (such as silica) and higher concentrations of solutes derived from the land surface (such as sulfate, nitrate and phosphorous).The two groundwater components represented shallow versus deep groundwater (as in IN, MD and WA), oxic versus anoxic GW (as in IA and MS), and groundwater from two different rock types (as in NE where groundwater from loess had higher solute concentrations than water from unconsolidated deposits). Examination of stream water chemistry for nested drainages within a single watershed indicated that the contribution from the deep (often anoxic) GW component increased as watershed size increased. The conclusions from this principal components and end-member-mixing analysis are being used to help identify and quantify the sources of nitrogen transport to the streams.

  14. Alternate dissociation pathways identified in charge-reduced protein complex ions.

    PubMed

    Pagel, Kevin; Hyung, Suk-Joon; Ruotolo, Brandon T; Robinson, Carol V

    2010-06-15

    Tandem mass spectrometry (MS) of large protein complexes has proven to be capable of assessing the stoichiometry, connectivity, and structural details of multiprotein assemblies. While the utility of tandem MS is without question, a deeper understanding of the mechanism of protein complex dissociation will undoubtedly drive the technology into new areas of enhanced utility and information content. We present here the systematic analysis of the charge state dependent decay of the noncovalently associated complex of human transthyretin, generated by collision-induced dissociation (CID). A crown ether based charge reduction approach was applied to generate intact transthyretin tetramers with charge states ranging from 15+ to 7+. These nine charge states were subsequently analyzed by means of tandem MS and ion mobility spectrometry. Three different charge-dependent mechanistic regimes were identified: (1) common asymmetric dissociation involving ejection of unfolded monomers, (2) expulsion of folded monomers from the intact tetramer, and (3) release of C-terminal peptide fragments from the intact complex. Taken together, the results presented highlight the potential of charge state modulation as a method for directing the course of gas-phase dissociation and unfolding of protein complexes. PMID:20481443

  15. Novel Host Proteins and Signaling Pathways in Enteropathogenic E. coli Pathogenesis Identified by Global Phosphoproteome Analysis.

    PubMed

    Scholz, Roland; Imami, Koshi; Scott, Nichollas E; Trimble, William S; Foster, Leonard J; Finlay, B Brett

    2015-07-01

    Enteropathogenic Escherichia coli (EPEC) uses a type III secretion system (T3SS) to directly translocate effector proteins into host cells where they play a pivotal role in subverting host cell signaling needed for disease. However, our knowledge of how EPEC affects host protein phosphorylation is limited to a few individual protein studies. We employed a quantitative proteomics approach to globally map alterations in the host phosphoproteome during EPEC infection. By characterizing host phosphorylation events at various time points throughout infection, we examined how EPEC dynamically impacts the host phosphoproteome over time. This experimental setup also enabled identification of T3SS-dependent and -independent changes in host phosphorylation. Specifically, T3SS-regulated events affected various cellular processes that are known EPEC targets, including cytoskeletal organization, immune signaling, and intracellular trafficking. However, the involvement of phosphorylation in these events has thus far been poorly studied. We confirmed the MAPK family as an established key host player, showed its central role in signal transduction during EPEC infection, and extended the repertoire of known signaling hubs with previously unrecognized proteins, including TPD52, CIN85, EPHA2, and HSP27. We identified altered phosphorylation of known EPEC targets, such as cofilin, where the involvement of phosphorylation has so far been undefined, thus providing novel mechanistic insights into the roles of these proteins in EPEC infection. An overlap of regulated proteins, especially those that are cytoskeleton-associated, was observed when compared with the phosphoproteome of Shigella-infected cells. We determined the biological relevance of the phosphorylation of a novel protein in EPEC pathogenesis, septin-9 (SEPT9). Both siRNA knockdown and a phosphorylation-impaired SEPT9 mutant decreased bacterial adherence and EPEC-mediated cell death. In contrast, a phosphorylation-mimicking SEPT9 mutant rescued these effects. Collectively, this study provides the first global analysis of phosphorylation-mediated processes during infection with an extracellular, diarrheagenic bacterial pathogen. PMID:25944883

  16. Structural and Logical Analysis of a Comprehensive Hedgehog Signaling Pathway to Identify Alternative Drug Targets for Glioma, Colon and Pancreatic Cancer

    PubMed Central

    Chowdhury, Saikat; Pradhan, Rachana N.; Sarkar, Ram Rup

    2013-01-01

    Hedgehog is an evolutionarily conserved developmental pathway, widely implicated in controlling various cellular responses such as cellular proliferation and stem cell renewal in human and other organisms, through external stimuli. Aberrant activation of this pathway in human adult stem cell line may cause different types of cancers. Hence, targeting this pathway in cancer therapy has become indispensable, but the non availability of detailed molecular interactions, complex regulations by extra- and intra-cellular proteins and cross talks with other pathways pose a serious challenge to get a coherent understanding of this signaling pathway for making therapeutic strategy. This motivated us to perform a computational study of the pathway and to identify probable drug targets. In this work, from available databases and literature, we reconstructed a complete hedgehog pathway which reports the largest number of molecules and interactions to date. Using recently developed computational techniques, we further performed structural and logical analysis of this pathway. In structural analysis, the connectivity and centrality parameters were calculated to identify the important proteins from the network. To capture the regulations of the molecules, we developed a master Boolean model of all the interactions between the proteins and created different cancer scenarios, such as Glioma, Colon and Pancreatic. We performed perturbation analysis on these cancer conditions to identify the important and minimal combinations of proteins that can be used as drug targets. From our study we observed the under expressions of various oncoproteins in Hedgehog pathway while perturbing at a time the combinations of the proteins GLI1, GLI2 and SMO in Glioma; SMO, HFU, ULK3 and RAS in Colon cancer; SMO, HFU, ULK3, RAS and ERK12 in Pancreatic cancer. This reconstructed Hedgehog signaling pathway and the computational analysis for identifying new combinatory drug targets will be useful for future in-vitro and in-vivo analysis to control different cancers. PMID:23935937

  17. Functional Genetic Screen Identifies Increased Sensitivity to WEE1 Inhibition in Cells with Defects in Fanconi Anemia and HR Pathways.

    PubMed

    Aarts, Marieke; Bajrami, Ilirjana; Herrera-Abreu, Maria T; Elliott, Richard; Brough, Rachel; Ashworth, Alan; Lord, Christopher J; Turner, Nicholas C

    2015-04-01

    WEE1 kinase regulates CDK1 and CDK2 activity to facilitate DNA replication during S-phase and to prevent unscheduled entry into mitosis. WEE1 inhibitors synergize with DNA-damaging agents that arrest cells in S-phase by triggering direct mitotic entry without completing DNA synthesis, resulting in catastrophic chromosome fragmentation and apoptosis. Here, we investigated how WEE1 inhibition could be best exploited for cancer therapy by performing a functional genetic screen to identify novel determinants of sensitivity to WEE1 inhibition. Inhibition of kinases that regulate CDK activity, CHK1 and MYT1, synergized with WEE1 inhibition through both increased replication stress and forced mitotic entry of S-phase cells. Loss of multiple components of the Fanconi anemia (FA) and homologous recombination (HR) pathways, in particular DNA helicases, sensitized to WEE1 inhibition. Silencing of FA/HR genes resulted in excessive replication stress and nucleotide depletion following WEE1 inhibition, which ultimately led to increased unscheduled mitotic entry. Our results suggest that cancers with defects in FA and HR pathways may be targeted by WEE1 inhibition, providing a basis for a novel synthetic lethal strategy for cancers harboring FA/HR defects. Mol Cancer Ther; 14(4); 865-76. ©2015 AACR. PMID:25673822

  18. Long-term consequences of pubertal timing for youth depression: Identifying personal and contextual pathways of risk.

    PubMed

    Rudolph, Karen D; Troop-Gordon, Wendy; Lambert, Sharon F; Natsuaki, Misaki N

    2014-11-01

    This research explored sex differences in the pathways linking pubertal timing to depression across 4 years. A sample of 167 youth (M age = 12.41 years, SD = 1.19) and their caregivers completed measures of puberty and semistructured interviews of interpersonal stress and youth depression. Youth reported on psychological (negative self-focus, anxious arousal) and social-behavioral (coping) characteristics; parents reported on youths' social-behavioral characteristics (withdrawal/social problems) and deviant peer affiliations. Early maturation predicted stable high trajectories of depression in girls; although early maturing boys showed low initial levels of depression, they did not differ from girls by the final wave of the study. Latent growth curve analyses identified several psychological, social-behavioral, and interpersonal pathways accounting for the contribution of pubertal timing to initial and enduring risk for depression in girls as well as emerging risk for depression in boys. These findings provide novel insight into multilevel processes accounting for sex differences in depression across the adolescent transition. PMID:25422971

  19. Adaptative biochemical pathways and regulatory networks in Klebsiella oxytoca BAS-10 producing a biotechnologically relevant exopolysaccharide during Fe(III)-citrate fermentation

    PubMed Central

    2012-01-01

    Background A bacterial strain previously isolated from pyrite mine drainage and named BAS-10 was tentatively identified as Klebsiella oxytoca. Unlikely other enterobacteria, BAS-10 is able to grow on Fe(III)-citrate as sole carbon and energy source, yielding acetic acid and CO2 coupled with Fe(III) reduction to Fe(II) and showing unusual physiological characteristics. In fact, under this growth condition, BAS-10 produces an exopolysaccharide (EPS) having a high rhamnose content and metal-binding properties, whose biotechnological applications were proven as very relevant. Results Further phylogenetic analysis, based on 16S rDNA sequence, definitively confirmed that BAS-10 belongs to K. oxytoca species. In order to rationalize the biochemical peculiarities of this unusual enterobacteriun, combined 2D-Differential Gel Electrophoresis (2D-DIGE) analysis and mass spectrometry procedures were used to investigate its proteomic changes: i) under aerobic or anaerobic cultivation with Fe(III)-citrate as sole carbon source; ii) under anaerobic cultivations using Na(I)-citrate or Fe(III)-citrate as sole carbon source. Combining data from these differential studies peculiar levels of outer membrane proteins, key regulatory factors of carbon and nitrogen metabolism and enzymes involved in TCA cycle and sugar biosynthesis or required for citrate fermentation and stress response during anaerobic growth on Fe(III)-citrate were revealed. The protein differential regulation seems to ensure efficient cell growth coupled with EPS production by adapting metabolic and biochemical processes in order to face iron toxicity and to optimize energy production. Conclusion Differential proteomics provided insights on the molecular mechanisms necessary for anaeorobic utilization of Fe(III)-citrate in a biotechnologically promising enterobacteriun, also revealing genes that can be targeted for the rational design of high-yielding EPS producer strains. PMID:23176641

  20. DrGaP: A Powerful Tool for Identifying Driver Genes and Pathways in Cancer Sequencing Studies

    PubMed Central

    Hua, Xing; Xu, Haiming; Yang, Yaning; Zhu, Jun; Liu, Pengyuan; Lu, Yan

    2013-01-01

    Cancers are caused by the accumulation of genomic alterations. Driver mutations are required for the cancer phenotype, whereas passenger mutations are irrelevant to tumor development and accumulate through DNA replication. A major challenge facing the field of cancer genome sequencing is to identify cancer-associated genes with mutations that drive the cancer phenotype. Here, we describe a powerful and flexible statistical framework for identifying driver genes and driver signaling pathways in cancer genome-sequencing studies. Biological knowledge of the mutational process in tumors is fully integrated into our statistical models and includes such variables as the length of protein-coding regions, transcript isoforms, variation in mutation types, differences in background mutation rates, the redundancy of genetic code, and multiple mutations in one gene. This framework provides several significant features that are not addressed or naively obtained by previous methods. In particular, on the observation of low prevalence of somatic mutations in individual tumors, we propose a heuristic strategy to estimate the mixture proportion of chi-square distribution of likelihood ratio test (LRT) statistics. This provides significantly increased statistical power compared to regular LRT. Through a combination of simulation and analysis of TCGA cancer sequencing study data, we demonstrate high accuracy and sensitivity in our methods. Our statistical methods and several auxiliary bioinformatics tools have been incorporated into a computational tool, DrGaP. The newly developed tool is immediately applicable to cancer genome-sequencing studies and will lead to a more complete identification of altered driver genes and driver signaling pathways in cancer. PMID:23954162

  1. Interactome analysis identifies a new paralogue of XRCC4 in non-homologous end joining DNA repair pathway.

    PubMed

    Xing, Mengtan; Yang, Mingrui; Huo, Wei; Feng, Feng; Wei, Leizhen; Jiang, Wenxia; Ning, Shaokai; Yan, Zhenxin; Li, Wen; Wang, Qingsong; Hou, Mei; Dong, Chunxia; Guo, Rong; Gao, Ge; Ji, Jianguo; Zha, Shan; Lan, Li; Liang, Huanhuan; Xu, Dongyi

    2015-01-01

    Non-homologous end joining (NHEJ) is a major pathway to repair DNA double-strand breaks (DSBs), which can display different types of broken ends. However, it is unclear how NHEJ factors organize to repair diverse types of DNA breaks. Here, through systematic analysis of the human NHEJ factor interactome, we identify PAXX as a direct interactor of Ku. The crystal structure of PAXX is similar to those of XRCC4 and XLF. Importantly, PAXX-deficient cells are sensitive to DSB-causing agents. Moreover, epistasis analysis demonstrates that PAXX functions together with XLF in response to ionizing radiation-induced complex DSBs, whereas they function redundantly in response to Topo2 inhibitor-induced simple DSBs. Consistently, PAXX and XLF coordinately promote the ligation of complex but not simple DNA ends in vitro. Altogether, our data identify PAXX as a new NHEJ factor and provide insight regarding the organization of NHEJ factors responding to diverse types of DSB ends. PMID:25670504

  2. Interactome analysis identifies a new paralogue of XRCC4 in non-homologous end joining DNA repair pathway

    PubMed Central

    Xing, Mengtan; Yang, Mingrui; Huo, Wei; Feng, Feng; Wei, Leizhen; Jiang, Wenxia; Ning, Shaokai; Yan, Zhenxin; Li, Wen; Wang, Qingsong; Hou, Mei; Dong, Chunxia; Guo, Rong; Gao, Ge; Ji, Jianguo; Zha, Shan; Lan, Li; Liang, Huanhuan; Xu, Dongyi

    2015-01-01

    Non-homologous end joining (NHEJ) is a major pathway to repair DNA double-strand breaks (DSBs), which can display different types of broken ends. However, it is unclear how NHEJ factors organize to repair diverse types of DNA breaks. Here, through systematic analysis of the human NHEJ factor interactome, we identify PAXX as a direct interactor of Ku. The crystal structure of PAXX is similar to those of XRCC4 and XLF. Importantly, PAXX-deficient cells are sensitive to DSB-causing agents. Moreover, epistasis analysis demonstrates that PAXX functions together with XLF in response to ionizing radiation-induced complex DSBs, whereas they function redundantly in response to Topo2 inhibitor-induced simple DSBs. Consistently, PAXX and XLF coordinately promote the ligation of complex but not simple DNA ends in vitro. Altogether, our data identify PAXX as a new NHEJ factor and provide insight regarding the organization of NHEJ factors responding to diverse types of DSB ends. PMID:25670504

  3. Construction and analysis of biochemical networks

    NASA Astrophysics Data System (ADS)

    Binns, Michael; Theodoropoulos, Constantinos

    2012-09-01

    Bioprocesses are being implemented for a range of different applications including the production of fuels, chemicals and drugs. Hence, it is becoming increasingly important to understand and model how they function and how they can be modified or designed to give the optimal performance. Here we discuss the construction and analysis of biochemical networks which are the first logical steps towards this goal. The construction of a reaction network is possible through reconstruction: extracting information from literature and from databases. This can be supplemented by reaction prediction methods which can identify steps which are missing from the current knowledge base. Analysis of biochemical systems generally requires some experimental input but can be used to identify important reactions and targets for enhancing the performance of the organism involved. Metabolic flux, pathway and metabolic control analysis can be used to determine the limits, capabilities and potential targets for enhancement respectively.

  4. Genome wide transcriptomic analysis identifies pathways affected by the infusion of culture supernatant in the duodenum of broilers in situ.

    PubMed

    Athanasiadou, S; Russell, K M; Kaiser, P; Kanellos, T; Burgess, S T G; Mitchell, M; Clutton, E; Naylor, S W; Low, C J; Hutchings, M R; Sparks, N

    2015-06-01

    type A is the main etiological factor for necrotic enteritis, a multifactorial enteric disease that penalizes performance, health, and welfare of poultry. Lack of knowledge of host responses and disease pathogenesis is slowing down progress on developing therapies for disease control. A combined genomewide and targeted gene approach was used to investigate pathways and biological functions affected by the infusion of culture supernatant in the duodenum of broilers in 2 experiments. An in situ isolated loop of duodenum was prepared in anesthetized broilers of 3 wk of age (Exp. 1) and was infused either with crude culture supernatant ( = 7; treated), positive for necrotic enteritis B-like toxin (NetB) as determined by a cytotoxicity assay, or with a control preparation ( = 6; control). Birds were maintained alive for 1 h and then euthanized for tissue recovery. The use of the Affymetrix chicken genome array on RNA samples from loop tissue showed top biological functions affected by culture supernatant infusion included cell morphology, immune cell trafficking, and cell death; pathways affected included death receptor signaling, inflammatory response, and nuclear factor (NF)-?B signaling. In a second in situ study (Exp. 2), broilers were maintained alive for 4 h to monitor temporal expression patterns of targeted genes. Duodenal tissue was removed at 0.5, 1, 2, and 4 h post-infusion with culture supernatant ( = 9) or a control preparation ( = 5) for histology and gene expression analysis. Genes encoding proinflammatory cytokines, such as interferon ? (?), cell trafficking, such as neuroblastoma 1 () and B cell CLL/Lymphoma 6 (), and cell death, such as Fas cell surface death receptor () and GTPase IMAP family member 8 (), were differentially expressed in the duodenum of treated and control broilers ( < 0.05). We have demonstrated that culture supernatant (NetB positive) infusion resulted in histological and gene expression changes consistent with necrotic enteritis in the duodenum of broilers. In the absence of live bacteria, crude culture supernatant resulted in early immunomodulation, inflammation, and cell death in the duodenum. The pathways identified here can be targeted for the development of new drugs, vaccines, and novel therapies for necrotic enteritis in broilers. PMID:26115301

  5. NETWORK RECONSTRUCTION OF BIOCHEMICAL PATHWAYS

    E-print Network

    Gunawardena, Jeremy

    function f : kN k is a polynomial #12;From the data to the network Discretize continuous data Select) = (y2 , y + 1, 2y ­ z + 1) Check: F(2, 2, 2) = (1, 0, 0) F(1, 0, 0) = (0, 1, 1) F F #12;Step 4: Select If the function for x coordinate depends on y, draw an edge from y to x. Our toy example: F(x, y, z) = (y2 , y

  6. Whole Blood Transcriptomics and Urinary Metabolomics to Define Adaptive Biochemical Pathways of High-Intensity Exercise in 50-60 Year Old Masters Athletes

    PubMed Central

    Mukherjee, Kamalika; Edgett, Brittany A.; Burrows, Harrison W.; Castro, Cecilia; Griffin, Julian L.; Schwertani, Adel Giaid; Gurd, Brendon J.; Funk, Colin D.

    2014-01-01

    Exercise is beneficial for a variety of age-related disorders. However, the molecular mechanisms mediating the beneficial adaptations to exercise in older adults are not well understood. The aim of the current study was to utilize a dual approach to characterize the genetic and metabolic adaptive pathways altered by exercise in veteran athletes and age-matched untrained individuals. Two groups of 50–60 year old males: competitive cyclists (athletes, n?=?9; VO2peak 59.1±5.2 ml·kg?1·min?1; peak aerobic power 383±39 W) and untrained, minimally active individuals (controls, n?=?8; VO2peak 35.9±9.7 ml·kg?1·min?1; peak aerobic power 230±57 W) were examined. All participants completed an acute bout of submaximal endurance exercise, and blood and urine samples pre- and post-exercise were analyzed for gene expression and metabolic changes utilizing genome-wide DNA microarray analysis and NMR spectroscopy-based metabolomics, respectively. Our results indicate distinct differences in gene and metabolite expression involving energy metabolism, lipids, insulin signaling and cardiovascular function between the two groups. These findings may lead to new insights into beneficial signaling pathways of healthy aging and help identify surrogate markers for monitoring exercise and training load. PMID:24643011

  7. Extragenic Suppressors of the Arabidopsis Det1 Mutant Identify Elements of Flowering-Time and Light-Response Regulatory Pathways

    PubMed Central

    Pepper, A. E.; Chory, J.

    1997-01-01

    Light regulation of seedling morphogenesis is mediated by photoreceptors that perceive red, far-red, blue and UV light. Photomorphogenetic mutants of Arabidopsis have identified several of the primary photoreceptors, as well as a set of negative regulators of seedling photomorphogenesis, including DET1, that appear to act downstream of the photoreceptors. To study the regulatory context in which DET1 acts to repress photomorphogenesis, we used a simple morphological screen to isolate extragenic mutations in six loci, designated ted (for reversal of the det phenotype), that partially or fully suppress the seedling morphological phenotype of det1-1. Genetic analyses indicate that mutations in the ted4 and ted5 loci identify new alleles of the previously described photomorphogenetic loci hy1 and hy5, respectively. Molecular analyses indicate that the ted mutations partially suppress the dark-grown gene expression phenotype of det1-1, and that the mechanism of suppression does not involve direct remediation of the splicing defect caused by the det1-1 mutation. The ted mutations also partially suppress the light-grown morphological phenotype of mature det1-1 plants, and ted1 and ted2 suppress a daylength insensitivity phenotype of det1. TED1, TED2 and TED3 are newly described genes, whose function appears closely associated with that of DET1. In addition, alleles of ted1 are associated with a moderate late-flowering phenotype, suggesting that TED1 plays a role in the pathways that regulate both seedling morphogenesis and the initiation of flowering. PMID:9093863

  8. Identifying opportunities for sexually transmitted infection prevention: analysis of critical points in the care pathways of patients with gonorrhoea.

    PubMed

    Abu-Rajab, K; Scoular, A; Church, S; Connell, J; Winter, A; Hart, G

    2009-03-01

    We applied the principles of Hazard Analysis and Critical Control Points (HACCP) to systematically analyse the care pathway of patients diagnosed with gonorrhoea to identify potential intervention opportunities for preventive action. Data were collected on individuals with culture-positive gonococcal infection during 27 February 2003 to 08 January 2004. Qualitative data were gathered within individual semi-structured interviews. Two hundred and twenty-three gonorrhoea patient episodes were evaluated. The median interval between presentation and treatment was significantly longer in females and men having sex with men (MSM), compared with heterosexual men (P = 0.002). Females were significantly more likely to be in regular relationships at the timepoint of perceived infection acquisition than heterosexuals or MSM (P < 0.0001). Four major themes emerged from the interviews: life-stage and infection risk, determinants of risk perception around sexual encounters, attitudes to preventing re-infection and condom use. These informed three potential 'critical control points': health-related attitudes/behaviours preceding infection; access to appropriate care and optimizing health promotion to prevent further infection. PMID:19255264

  9. Pathway alignment: application to the comparative analysis of glycolytic enzymes.

    PubMed Central

    Dandekar, T; Schuster, S; Snel, B; Huynen, M; Bork, P

    1999-01-01

    Comparative analysis of metabolic pathways in different genomes yields important information on their evolution, on pharmacological targets and on biotechnological applications. In this study on glycolysis, three alternative ways of comparing biochemical pathways are combined: (1) analysis and comparison of biochemical data, (2) pathway analysis based on the concept of elementary modes, and (3) a comparative genome analysis of 17 completely sequenced genomes. The analysis reveals a surprising plasticity of the glycolytic pathway. Isoenzymes in different species are identified and compared; deviations from the textbook standard are detailed. Several potential pharmacological targets and by-passes (such as the Entner-Doudoroff pathway) to glycolysis are examined and compared in the different species. Archaean, bacterial and parasite specific adaptations are identified and described. PMID:10493919

  10. Proteomic profiling of naïve multiple myeloma patient plasma cells identifies pathways associated with favourable response to bortezomib-based treatment regimens.

    PubMed

    Dytfeld, Dominik; Rosebeck, Shaun; Kandarpa, Malathi; Mayampurath, Anoop; Mellacheruvu, Dattatreya; Alonge, Mattina M; Ngoka, Lambert; Jasielec, Jagoda; Richardson, Paul G; Volchenboum, Samuel; Nesvizhskii, Alexey I; Sreekumar, Arun; Jakubowiak, Andrzej J

    2015-07-01

    Toward our goal of personalized medicine, we comprehensively profiled pre-treatment malignant plasma cells from multiple myeloma patients and prospectively identified pathways predictive of favourable response to bortezomib-based treatment regimens. We utilized two complementary quantitative proteomics platforms to identify differentially-regulated proteins indicative of at least a very good partial response (VGPR) or complete response/near complete response (CR/nCR) to two treatment regimens containing either bortezomib, liposomal doxorubicin and dexamethasone (VDD), or lenalidomide, bortezomib and dexamethasone (RVD). Our results suggest enrichment of 'universal response' pathways that are common to both treatment regimens and are probable predictors of favourable response to bortezomib, including a subset of endoplasmic reticulum stress pathways. The data also implicate pathways unique to each regimen that may predict sensitivity to DNA-damaging agents, such as mitochondrial dysfunction, and immunomodulatory drugs, which was associated with acute phase response signalling. Overall, we identified patterns of tumour characteristics that may predict response to bortezomib-based regimens and their components. These results provide a rationale for further evaluation of the protein profiles identified herein for targeted selection of anti-myeloma therapy to increase the likelihood of improved treatment outcome of patients with newly-diagnosed myeloma. PMID:25824111

  11. A Functional Genome-Wide In Vivo Screen Identifies New Regulators of Signalling Pathways during Early Xenopus

    E-print Network

    Amaya, Enrique

    a relatively small number of signalling pathways, such as the Hedgehog, Wnt, Transforming Growth Factor-b (TGF-b), Bone Morphogenic Protein (BMP), Receptor Tyrosine Kinase (RTK), Notch, JAK/STAT and nuclear hormone

  12. New Variants Including ARG1 Polymorphisms Associated with C-Reactive Protein Levels Identified by Genome-Wide Association and Pathway Analysis

    PubMed Central

    Yim, Seon-Hee; Jung, Seung-Hyun; Jo, Jaeseong; Jee, Sun Ha; Chung, Yeun-Jun

    2014-01-01

    C-reactive protein (CRP) is a general marker of systemic inflammation and cardiovascular disease (CVD). The genetic contribution to differences in CRP levels remains to be explained, especially in non-European populations. Thus, the aim of this study was to identify genetic loci associated with CRP levels in Korean population. We performed genome-wide association studies (GWAS) using SNPs from 8,529 Korean individuals (7,626 for stage 1 and 903 for stage 2). We also performed pathway analysis. We identified a new genetic locus associated with CRP levels upstream of ARG1 gene (top significant SNP: rs9375813, Pmeta?=?2.85×10?8), which encodes a key enzyme of the urea cycle counteract the effects of nitric oxide, in addition to known CRP (rs7553007, Pmeta?=?1.72×10?16) and HNF1A loci (rs2259816, Pmeta?=?2.90×10?10). When we evaluated the associations between the CRP-related SNPs with cardiovascular disease phenotypes, rs9375813 (ARG1) showed a marginal association with hypertension (P?=?0.0440). To identify more variants and pathways, we performed pathway analysis and identified six candidate pathways comprised of genes related to inflammatory processes and CVDs (CRP, HNF1A, PCSK6, CD36, and ABCA1). In addition to the previously reported loci (CRP, HNF1A, and IL6) in diverse ethnic groups, we identified novel variants in the ARG1 locus associated with CRP levels in Korean population and a number of interesting genes related to inflammatory processes and CVD through pathway analysis. PMID:24763700

  13. Multiplexing oscillatory biochemical signals

    NASA Astrophysics Data System (ADS)

    de Ronde, Wiet; Rein ten Wolde, Pieter

    2014-04-01

    In recent years it has been increasingly recognized that biochemical signals are not necessarily constant in time and that the temporal dynamics of a signal can be the information carrier. Moreover, it is now well established that the protein signaling network of living cells has a bow-tie structure and that components are often shared between different signaling pathways. Here we show by mathematical modeling that living cells can multiplex a constant and an oscillatory signal: they can transmit these two signals simultaneously through a common signaling pathway, and yet respond to them specifically and reliably. We find that information transmission is reduced not only by noise arising from the intrinsic stochasticity of biochemical reactions, but also by crosstalk between the different channels. Yet, under biologically relevant conditions more than 2 bits of information can be transmitted per channel, even when the two signals are transmitted simultaneously. These observations suggest that oscillatory signals are ideal for multiplexing signals.

  14. Transcriptome Analysis in Prenatal IGF1-Deficient Mice Identifies Molecular Pathways and Target Genes Involved in Distal Lung Differentiation

    PubMed Central

    Hernández-Porras, Isabel; López, Icíar Paula; De Las Rivas, Javier; Pichel, José García

    2013-01-01

    Background Insulin-like Growth Factor 1 (IGF1) is a multifunctional regulator of somatic growth and development throughout evolution. IGF1 signaling through IGF type 1 receptor (IGF1R) controls cell proliferation, survival and differentiation in multiple cell types. IGF1 deficiency in mice disrupts lung morphogenesis, causing altered prenatal pulmonary alveologenesis. Nevertheless, little is known about the cellular and molecular basis of IGF1 activity during lung development. Methods/Principal Findings Prenatal Igf1?/? mutant mice with a C57Bl/6J genetic background displayed severe disproportional lung hypoplasia, leading to lethal neonatal respiratory distress. Immuno-histological analysis of their lungs showed a thickened mesenchyme, alterations in extracellular matrix deposition, thinner smooth muscles and dilated blood vessels, which indicated immature and delayed distal pulmonary organogenesis. Transcriptomic analysis of Igf1?/? E18.5 lungs using RNA microarrays identified deregulated genes related to vascularization, morphogenesis and cellular growth, and to MAP-kinase, Wnt and cell-adhesion pathways. Up-regulation of immunity-related genes was verified by an increase in inflammatory markers. Increased expression of Nfib and reduced expression of Klf2, Egr1 and Ctgf regulatory proteins as well as activation of ERK2 MAP-kinase were corroborated by Western blot. Among IGF-system genes only IGFBP2 revealed a reduction in mRNA expression in mutant lungs. Immuno-staining patterns for IGF1R and IGF2, similar in both genotypes, correlated to alterations found in specific cell compartments of Igf1?/? lungs. IGF1 addition to Igf1?/? embryonic lungs cultured ex vivo increased airway septa remodeling and distal epithelium maturation, processes accompanied by up-regulation of Nfib and Klf2 transcription factors and Cyr61 matricellular protein. Conclusions/Significance We demonstrated the functional tissue specific implication of IGF1 on fetal lung development in mice. Results revealed novel target genes and gene networks mediators of IGF1 action on pulmonary cellular proliferation, differentiation, adhesion and immunity, and on vascular and distal epithelium maturation during prenatal lung development. PMID:24391734

  15. Identifiers Identifiers

    E-print Network

    Brass, Stefan

    , July 1998. . Tim Berners­Lee: Cool URIs don't change. [http://www.w3.org/Provider/Style/URI] . Uniform://archive.ncsa.uiuc.edu/demoweb/url­primer.html] . T. Berners­Lee, R. Fielding, L. Masinter: Uniform Resource Identifiers (URI): Generic Syntax. RFC Names. RFC 1737, December 1994, 7 pages. . T. Berners­Lee, L. Masinter, M. McCahill: Uniform Resource

  16. Identifiers Identifiers

    E-print Network

    Brass, Stefan

    , July 1998. . Tim Berners­Lee: Cool URIs don't change. [http://www.w3.org/Provider/Style/URI] Stefan://archive.ncsa.uiuc.edu/demoweb/url­primer.html] . T. Berners­Lee, R. Fielding, L. Masinter: Uniform Resource Identifiers (URI): Generic Syntax. RFC Names. RFC 1737, December 1994, 7 pages. . T. Berners­Lee, L. Masinter, M. McCahill: Uniform Resource

  17. Pharmacological Inhibition of Nicotinamide Phosphoribosyltransferase\\/Visfatin Enzymatic Activity Identifies a New Inflammatory Pathway Linked to NAD

    Microsoft Academic Search

    Nathalie Busso; Mahir Karababa; Massimo Nobile; Aline Rolaz; Frédéric van Gool; Mara Galli; Oberdan Leo; Alexander So; Thibaut de Smedt; Jacques Zimmer

    2008-01-01

    Nicotinamide phosphoribosyltransferase (NAMPT), also known as visfatin, is the rate-limiting enzyme in the salvage pathway of NAD biosynthesis from nicotinamide. Since its expression is upregulated during inflammation, NAMPT represents a novel clinical biomarker in acute lung injury, rheumatoid arthritis, and Crohn's disease. However, its role in disease progression remains unknown. We report here that NAMPT is a key player in

  18. UTSW Investigators Develop Functional Signature Ontology (FUSION), a Method for Identifying Compounds That Target Cancer Pathways | Office of Cancer Genomics

    Cancer.gov

    In a new study published in Science Signaling, CTD2 investigators from University of Texas (UTSW) Southwestern Medical Center devised a novel bioinformatics approach that, when coupled with high-throughput screening, helps reveal compounds that may target potential cancer-related pathways.

  19. A large-scale RNAi screen in human cells identifies new components of the p53 pathway

    Microsoft Academic Search

    Katrien Berns; E. Marielle Hijmans; Jasper Mullenders; Thijn R. Brummelkamp; Arno Velds; Mike Heimerikx; Ron M. Kerkhoven; Mandy Madiredjo; Wouter Nijkamp; Britta Weigelt; Reuven Agami; Wei Ge; Guy Cavet; Peter S. Linsley; Roderick L. Beijersbergen; René Bernards

    2004-01-01

    RNA interference (RNAi) is a powerful new tool with which to perform loss-of-function genetic screens in lower organisms and can greatly facilitate the identification of components of cellular signalling pathways. In mammalian cells, such screens have been hampered by a lack of suitable tools that can be used on a large scale. We and others have recently developed expression vectors

  20. Native fluorescence spectroscopy of blood plasma of rats with experimental diabetes: identifying fingerprints of glucose-related metabolic pathways.

    PubMed

    Shirshin, Evgeny; Cherkasova, Olga; Tikhonova, Tatiana; Berlovskaya, Elena; Priezzhev, Alexander; Fadeev, Victor

    2015-05-01

    We present the results of a native fluorescence spectroscopy study of blood plasma of rats with experimental diabetes. It was shown that the fluorescence emission band shape at 320 nm excitation is the most indicative of hyperglycemia in the blood plasma samples. We provide the interpretation of this fact based on the changes in reduced nicotinamide adenine dinucleotide phosphate concentration due to glucose-related metabolic pathways and protein fluorescent cross-linking formation following nonenzymatic glycation. PMID:25692658

  1. Implementation of a High-Throughput Screen for Identifying Small Molecules to Activate the Keap1-Nrf2-ARE Pathway

    E-print Network

    Wu, Kai Connie; McDonald, Peter R.; Liu, Jie Jerry; Chaguturu, Rathnam; Klaassen, Curtis D.

    2012-10-08

    compounds protect against oxidative/ electrophilic stress-induced toxicity, at least partially through activating Nrf2. For example, curcumin protects against focal ischemia of the cerebrum through upregulation of Nrf2 [16], and oltipraz protects against... pathway [18]. To date, a number of compounds with diverse chemical structures have been shown to activate Keap1- Nrf2, including oxidizable diphenols (tBHQ), dithiolethiones (oltipraz), isothiocyanates (sulforaphane), and Michael acceptors (curcumin...

  2. A Synthetic Lethal Screen Identifies DNA Repair Pathways that Sensitize Cancer Cells to Combined ATR Inhibition and Cisplatin Treatments

    PubMed Central

    Mohni, Kareem N.; Thompson, Petria S.; Luzwick, Jessica W.; Glick, Gloria G.; Pendleton, Christopher S.; Lehmann, Brian D.; Pietenpol, Jennifer A.; Cortez, David

    2015-01-01

    The DNA damage response kinase ATR may be a useful cancer therapeutic target. ATR inhibition synergizes with loss of ERCC1, ATM, XRCC1 and DNA damaging chemotherapy agents. Clinical trials have begun using ATR inhibitors in combination with cisplatin. Here we report the first synthetic lethality screen with a combination treatment of an ATR inhibitor (ATRi) and cisplatin. Combination treatment with ATRi/cisplatin is synthetically lethal with loss of the TLS polymerase ? and 53BP1. Other DNA repair pathways including homologous recombination and mismatch repair do not exhibit synthetic lethal interactions with ATRi/cisplatin, even though loss of some of these repair pathways sensitizes cells to cisplatin as a single-agent. We also report that ATRi strongly synergizes with PARP inhibition, even in homologous recombination-proficient backgrounds. Lastly, ATR inhibitors were able to resensitize cisplatin-resistant cell lines to cisplatin. These data provide a comprehensive analysis of DNA repair pathways that exhibit synthetic lethality with ATR inhibitors when combined with cisplatin chemotherapy, and will help guide patient selection strategies as ATR inhibitors progress into the cancer clinic. PMID:25965342

  3. A Synthetic Lethal Screen Identifies DNA Repair Pathways that Sensitize Cancer Cells to Combined ATR Inhibition and Cisplatin Treatments.

    PubMed

    Mohni, Kareem N; Thompson, Petria S; Luzwick, Jessica W; Glick, Gloria G; Pendleton, Christopher S; Lehmann, Brian D; Pietenpol, Jennifer A; Cortez, David

    2015-01-01

    The DNA damage response kinase ATR may be a useful cancer therapeutic target. ATR inhibition synergizes with loss of ERCC1, ATM, XRCC1 and DNA damaging chemotherapy agents. Clinical trials have begun using ATR inhibitors in combination with cisplatin. Here we report the first synthetic lethality screen with a combination treatment of an ATR inhibitor (ATRi) and cisplatin. Combination treatment with ATRi/cisplatin is synthetically lethal with loss of the TLS polymerase ? and 53BP1. Other DNA repair pathways including homologous recombination and mismatch repair do not exhibit synthetic lethal interactions with ATRi/cisplatin, even though loss of some of these repair pathways sensitizes cells to cisplatin as a single-agent. We also report that ATRi strongly synergizes with PARP inhibition, even in homologous recombination-proficient backgrounds. Lastly, ATR inhibitors were able to resensitize cisplatin-resistant cell lines to cisplatin. These data provide a comprehensive analysis of DNA repair pathways that exhibit synthetic lethality with ATR inhibitors when combined with cisplatin chemotherapy, and will help guide patient selection strategies as ATR inhibitors progress into the cancer clinic. PMID:25965342

  4. Experimentally-Derived Fibroblast Gene Signatures Identify Molecular Pathways Associated with Distinct Subsets of Systemic Sclerosis Patients in Three Independent Cohorts

    PubMed Central

    Johnson, Michael E.; Mahoney, J. Matthew; Taroni, Jaclyn; Sargent, Jennifer L.; Marmarelis, Eleni; Wu, Ming-Ru; Varga, John; Hinchcliff, Monique E.; Whitfield, Michael L.

    2015-01-01

    Genome-wide expression profiling in systemic sclerosis (SSc) has identified four ‘intrinsic’ subsets of disease (fibroproliferative, inflammatory, limited, and normal-like), each of which shows deregulation of distinct signaling pathways; however, the full set of pathways contributing to this differential gene expression has not been fully elucidated. Here we examine experimentally derived gene expression signatures in dermal fibroblasts for thirteen different signaling pathways implicated in SSc pathogenesis. These data show distinct and overlapping sets of genes induced by each pathway, allowing for a better understanding of the molecular relationship between profibrotic and immune signaling networks. Pathway-specific gene signatures were analyzed across a compendium of microarray datasets consisting of skin biopsies from three independent cohorts representing 80 SSc patients, 4 morphea, and 26 controls. IFN? signaling showed a strong association with early disease, while TGF? signaling spanned the fibroproliferative and inflammatory subsets, was associated with worse MRSS, and was higher in lesional than non-lesional skin. The fibroproliferative subset was most strongly associated with PDGF signaling, while the inflammatory subset demonstrated strong activation of innate immune pathways including TLR signaling upstream of NF-?B. The limited and normal-like subsets did not show associations with fibrotic and inflammatory mediators such as TGF? and TNF?. The normal-like subset showed high expression of genes associated with lipid signaling, which was absent in the inflammatory and limited subsets. Together, these data suggest a model by which IFN? is involved in early disease pathology, and disease severity is associated with active TGF? signaling. PMID:25607805

  5. Experimentally-derived fibroblast gene signatures identify molecular pathways associated with distinct subsets of systemic sclerosis patients in three independent cohorts.

    PubMed

    Johnson, Michael E; Mahoney, J Matthew; Taroni, Jaclyn; Sargent, Jennifer L; Marmarelis, Eleni; Wu, Ming-Ru; Varga, John; Hinchcliff, Monique E; Whitfield, Michael L

    2015-01-01

    Genome-wide expression profiling in systemic sclerosis (SSc) has identified four 'intrinsic' subsets of disease (fibroproliferative, inflammatory, limited, and normal-like), each of which shows deregulation of distinct signaling pathways; however, the full set of pathways contributing to this differential gene expression has not been fully elucidated. Here we examine experimentally derived gene expression signatures in dermal fibroblasts for thirteen different signaling pathways implicated in SSc pathogenesis. These data show distinct and overlapping sets of genes induced by each pathway, allowing for a better understanding of the molecular relationship between profibrotic and immune signaling networks. Pathway-specific gene signatures were analyzed across a compendium of microarray datasets consisting of skin biopsies from three independent cohorts representing 80 SSc patients, 4 morphea, and 26 controls. IFN? signaling showed a strong association with early disease, while TGF? signaling spanned the fibroproliferative and inflammatory subsets, was associated with worse MRSS, and was higher in lesional than non-lesional skin. The fibroproliferative subset was most strongly associated with PDGF signaling, while the inflammatory subset demonstrated strong activation of innate immune pathways including TLR signaling upstream of NF-?B. The limited and normal-like subsets did not show associations with fibrotic and inflammatory mediators such as TGF? and TNF?. The normal-like subset showed high expression of genes associated with lipid signaling, which was absent in the inflammatory and limited subsets. Together, these data suggest a model by which IFN? is involved in early disease pathology, and disease severity is associated with active TGF? signaling. PMID:25607805

  6. Method for identifying subsurface fluid migration and drainage pathways in and among oil and gas reservoirs using 3-D and 4-D seismic imaging

    DOEpatents

    Anderson, Roger N. (New York, NY); Boulanger, Albert (New York, NY); Bagdonas, Edward P. (Brookline, MA); Xu, Liqing (New Milford, NJ); He, Wei (New Milford, NJ)

    1996-01-01

    The invention utilizes 3-D and 4-D seismic surveys as a means of deriving information useful in petroleum exploration and reservoir management. The methods use both single seismic surveys (3-D) and multiple seismic surveys separated in time (4-D) of a region of interest to determine large scale migration pathways within sedimentary basins, and fine scale drainage structure and oil-water-gas regions within individual petroleum producing reservoirs. Such structure is identified using pattern recognition tools which define the regions of interest. The 4-D seismic data sets may be used for data completion for large scale structure where time intervals between surveys do not allow for dynamic evolution. The 4-D seismic data sets also may be used to find variations over time of small scale structure within individual reservoirs which may be used to identify petroleum drainage pathways, oil-water-gas regions and, hence, attractive drilling targets. After spatial orientation, and amplitude and frequency matching of the multiple seismic data sets, High Amplitude Event (HAE) regions consistent with the presence of petroleum are identified using seismic attribute analysis. High Amplitude Regions are grown and interconnected to establish plumbing networks on the large scale and reservoir structure on the small scale. Small scale variations over time between seismic surveys within individual reservoirs are identified and used to identify drainage patterns and bypassed petroleum to be recovered. The location of such drainage patterns and bypassed petroleum may be used to site wells.

  7. Method for identifying subsurface fluid migration and drainage pathways in and among oil and gas reservoirs using 3-D and 4-D seismic imaging

    DOEpatents

    Anderson, R.N.; Boulanger, A.; Bagdonas, E.P.; Xu, L.; He, W.

    1996-12-17

    The invention utilizes 3-D and 4-D seismic surveys as a means of deriving information useful in petroleum exploration and reservoir management. The methods use both single seismic surveys (3-D) and multiple seismic surveys separated in time (4-D) of a region of interest to determine large scale migration pathways within sedimentary basins, and fine scale drainage structure and oil-water-gas regions within individual petroleum producing reservoirs. Such structure is identified using pattern recognition tools which define the regions of interest. The 4-D seismic data sets may be used for data completion for large scale structure where time intervals between surveys do not allow for dynamic evolution. The 4-D seismic data sets also may be used to find variations over time of small scale structure within individual reservoirs which may be used to identify petroleum drainage pathways, oil-water-gas regions and, hence, attractive drilling targets. After spatial orientation, and amplitude and frequency matching of the multiple seismic data sets, High Amplitude Event (HAE) regions consistent with the presence of petroleum are identified using seismic attribute analysis. High Amplitude Regions are grown and interconnected to establish plumbing networks on the large scale and reservoir structure on the small scale. Small scale variations over time between seismic surveys within individual reservoirs are identified and used to identify drainage patterns and bypassed petroleum to be recovered. The location of such drainage patterns and bypassed petroleum may be used to site wells. 22 figs.

  8. Systematic CpG Islands Methylation Profiling of Genes in the Wnt Pathway in Epithelial Ovarian Cancer Identifies Biomarkers of Progression-Free Survival

    PubMed Central

    Dai, Wei; Teodoridis, Jens M.; Zeller, Constanze; Graham, Janet; Hersey, Jenny; Flanagan, James M.; Stronach, Euan; Millan, David W.; Siddiqui, Nadeem; Paul, Jim; Brown, Robert

    2011-01-01

    Purpose Wnt pathways control key biological processes that potentially impact on tumour progression and patient survival. We aimed to evaluate DNA methylation at promoter CpG islands (CGIs) of Wnt pathway genes in ovarian tumours at presentation and identify biomarkers of patient progression-free survival (PFS). Experimental Design Epithelial ovarian tumours (screening study n=120, validation study n=61) prospectively collected through a cohort study, were analysed by differential methylation hybridisation (DMH) at 302 loci spanning 189 promoter CGIs at 137 genes in Wnt pathways. The association of methylation and progression free survival was examined by Cox proportional hazards model. Results DNA methylation is associated with PFS at 20/302 loci (p<0.05, n=111), with 5 loci significant at FDR<10%. 11/20 loci retain significance in an independent validation cohort (n=48,p?0.05,FDR?10%), and 7 of these loci, at FZD4, DVL1, NFATC3, ROCK1, LRP5, AXIN1 and NKD1 genes, are independent from clinical parameters (adjusted p<0.05). Increased methylation at these loci associates with increased hazard of disease progression. A multivariate Cox model incorporates only NKD1 and DVL1, identifying two groups differing in PFS (HR=2.09; 95%CI (1.39, 3.15); permutation test p<0.005). Methylation at DVL1 and NFATC3 show significant association with response. Consistent with their epigenetic regulation, reduced expression of FZD4, DVL1 and ROCK1 is an indicator of early disease relapse in an independent ovarian tumour cohort (n=311, adjusted p<0.05). Conclusions The data highlights the importance of epigenetic regulation of multiple promoter CGIs of Wnt pathway genes in ovarian cancer and identifies methylation at NKD1 and DVL1 as independent predictors of PFS. PMID:21459799

  9. Utilising conservative tracers and spatial surveys to identify controls on pathways and DOC exports in an Arctic catchment.

    NASA Astrophysics Data System (ADS)

    Lessels, J. S.; Tetzlaff, D.; Dinsmore, K. J.; Street, L. E.; Dean, J.; Washbourne, I. J.; Billett, M. F.; Baxter, R.; Subke, J. A.; Wookey, P. A.

    2014-12-01

    Dissolved organic carbon (DOC) is typically the predominant form of carbon exported from headwater streams, it therefore represents a major carbon export from Arctic catchments. The projected deepening of thaw depth in permafrost regions, due to an increase in air temperature, may have a significant effect on the amount of DOC exported from these systems. However, quantification of the impacts of climate driven changes on DOC export are still highly uncertain. Understanding the processes controlling DOC export is therefore crucial in predicting the potential impact of projected environmental changes. The controls of DOC production and transport are heavily influenced by soil and vegetation, which are highly variable across the landscape. To completely understand these systems information regarding spatial variability of plants, soils and thaw depths must be taken into account. In this study sub-weekly sampling of DOC was undertaken throughout 2014 in a headwater (<1 km2) catchment in the Northwest Territories, Canada. Spatial surveys of soil properties, active thaw depth and normalised difference vegetation index (NDVI) were collected and used in conjunction with conservative stable water isotopes tracers and major ions to understand sources, flow pathways and timing of DOC exports from the catchment. Stable isotope tracers act as fingerprints of water allowing sources and pathways to be assessed. Observations reveal changing DOC concentrations throughout the season as the active layer deepens and the connectivity of the soils to the stream network throughout the catchment increases. Linking the DOC data with the conservative tracer response improves the identification of carbon pathways and fluxes from the soils; preliminary analysis indicates DOC is being delivered via deeper more mineral soils later in the season. The results indicate that the active layer depth has a strong influence on the amount of DOC exported from the system, independent of the amount of carbon stored in these deeper soils.

  10. A sensitized genetic screen to identify novel regulators and components of the Drosophila janus kinase/signal transducer and activator of transcription pathway.

    PubMed Central

    Bach, Erika A; Vincent, Stephane; Zeidler, Martin P; Perrimon, Norbert

    2003-01-01

    The JAK/STAT pathway exerts pleiotropic effects on a wide range of developmental processes in Drosophila. Four key components have been identified: Unpaired, a secreted ligand; Domeless, a cytokine-like receptor; Hopscotch, a JAK kinase; and Stat92E, a STAT transcription factor. The identification of additional components and regulators of this pathway remains an important issue. To this end, we have generated a transgenic line where we misexpress the upd ligand in the developing Drosophila eye. GMR-upd transgenic animals have dramatically enlarged eye-imaginal discs and compound eyes that are normally patterned. We demonstrate that the enlarged-eye phenotype is a result of an increase in cell number, and not cell volume, and arises from additional mitoses in larval eye discs. Thus, the GMR-upd line represents a system in which the proliferation and differentiation of eye precursor cells are separable. Removal of one copy of stat92E substantially reduces the enlarged-eye phenotype. We performed an F1 deficiency screen to identify dominant modifiers of the GMR-upd phenotype. We have identified 9 regions that enhance this eye phenotype and two specific enhancers: C-terminal binding protein and Daughters against dpp. We also identified 20 regions that suppress GMR-upd and 13 specific suppressors: zeste-white 13, pineapple eye, Dichaete, histone 2A variant, headcase, plexus, kohtalo, crumbs, hedgehog, decapentaplegic, thickveins, saxophone, and Mothers against dpp. PMID:14668372

  11. Identifying viable regulatory and innovation pathways for regenerative medicine: a case study of cultured red blood cells.

    PubMed

    Mittra, J; Tait, J; Mastroeni, M; Turner, M L; Mountford, J C; Bruce, K

    2015-01-25

    The creation of red blood cells for the blood transfusion markets represents a highly innovative application of regenerative medicine with a medium term (5-10 year) prospect for first clinical studies. This article describes a case study analysis of a project to derive red blood cells from human embryonic stem cells, including the systemic challenges arising from (i) the selection of appropriate and viable regulatory protocols and (ii) technological constraints related to stem cell manufacture and scale up to clinical Good Manufacturing Practice (GMP) standard. The method used for case study analysis (Analysis of Life Science Innovation Systems (ALSIS)) is also innovative, demonstrating a new approach to social and natural science collaboration to foresight product development pathways. Issues arising along the development pathway include cell manufacture and scale-up challenges, affected by regulatory demands emerging from the innovation ecosystem (preclinical testing and clinical trials). Our discussion reflects on the efforts being made by regulators to adapt the current pharmaceuticals-based regulatory model to an allogeneic regenerative medicine product and the broader lessons from this case study for successful innovation and translation of regenerative medicine therapies, including the role of methodological and regulatory innovation in future development in the field. PMID:25094050

  12. Patient-Based Transcriptome-Wide Analysis Identify Interferon and Ubiquination Pathways as Potential Predictors of Influenza A Disease Severity

    PubMed Central

    Hoang, Long Truong; Tolfvenstam, Thomas; Ooi, Eng Eong; Khor, Chiea Chuen; Naim, Ahmand Nazri Mohamed; Ho, Eliza Xin Pei; Ong, Swee Hoe; Wertheim, Heiman F.; Fox, Annette; Van Vinh Nguyen, Chau; Nghiem, Ngoc My; Ha, Tuan Manh; Thi Ngoc Tran, Anh; Tambayah, Paul; Lin, Raymond; Sangsajja, Chariya; Manosuthi, Weerawat; Chuchottaworn, Chareon; Sansayunh, Piamlarp; Chotpitayasunondh, Tawee; Suntarattiwong, Piyarat; Chokephaibulkit, Kulkanya; Puthavathana, Pilaipan; de Jong, Menno D.; Farrar, Jeremy; van Doorn, H. Rogier; Hibberd, Martin Lloyd

    2014-01-01

    Background The influenza A virus is an RNA virus that is responsible for seasonal epidemics worldwide with up to five million cases of severe illness and 500,000 deaths annually according to the World Health Organization estimates. The factors associated with severe diseases are not well defined, but more severe disease is more often seen among persons aged >65 years, infants, pregnant women, and individuals of any age with underlying health conditions. Methodology/Principal Findings Using gene expression microarrays, the transcriptomic profiles of influenza-infected patients with severe (N?=?11), moderate (N?=?40) and mild (N?=?83) symptoms were compared with the febrile patients of unknown etiology (N?=?73). We found that influenza-infected patients, regardless of their clinical outcomes, had a stronger induction of antiviral and cytokine responses and a stronger attenuation of NK and T cell responses in comparison with those with unknown etiology. More importantly, we found that both interferon and ubiquitination signaling were strongly attenuated in patients with the most severe outcomes in comparison with those with moderate and mild outcomes, suggesting the protective roles of these pathways in disease pathogenesis. Conclusion/Significances The attenuation of interferon and ubiquitination pathways may associate with the clinical outcomes of influenza patients. PMID:25365328

  13. Drug Intervention Response Predictions with PARADIGM (DIRPP) identifies drug resistant cancer cell lines and pathway mechanisms of resistance.

    PubMed

    Brubaker, Douglas; Difeo, Analisa; Chen, Yanwen; Pearl, Taylor; Zhai, Kaide; Bebek, Gurkan; Chance, Mark; Barnholtz-Sloan, Jill

    2014-01-01

    The revolution in sequencing techniques in the past decade has provided an extensive picture of the molecular mechanisms behind complex diseases such as cancer. The Cancer Cell Line Encyclopedia (CCLE) and The Cancer Genome Project (CGP) have provided an unprecedented opportunity to examine copy number, gene expression, and mutational information for over 1000 cell lines of multiple tumor types alongside IC50 values for over 150 different drugs and drug related compounds. We present a novel pipeline called DIRPP, Drug Intervention Response Predictions with PARADIGM7, which predicts a cell line's response to a drug intervention from molecular data. PARADIGM (Pathway Recognition Algorithm using Data Integration on Genomic Models) is a probabilistic graphical model used to infer patient specific genetic activity by integrating copy number and gene expression data into a factor graph model of a cellular network. We evaluated the performance of DIRPP on endometrial, ovarian, and breast cancer related cell lines from the CCLE and CGP for nine drugs. The pipeline is sensitive enough to predict the response of a cell line with accuracy and precision across datasets as high as 80 and 88% respectively. We then classify drugs by the specific pathway mechanisms governing drug response. This classification allows us to compare drugs by cellular response mechanisms rather than simply by their specific gene targets. This pipeline represents a novel approach for predicting clinical drug response and generating novel candidates for drug repurposing and repositioning. PMID:24297540

  14. Biosynthetic Pathway of Cephabacins in Lysobacter lactamgenus: Molecular and Biochemical Characterization of the Upstream Region of the Gene Clusters for Engineering of Novel Antibiotics

    Microsoft Academic Search

    Young-Sun Sohn; Doo-Hyun Nam; Dewey D. Y. Ryu

    2001-01-01

    The cephabacins, one of the ?-lactam antibiotics, are produced by Lysobacter lactamgenus. The previous studies the cephabacin biosynthesis were limited to a gene cluster that encodes the gene products responsible for the biosynthesis of the cephem nucleus. The long-term goal of this research is to elucidate the metabolic diversity and biosynthetic pathway of cephabacins and to design and\\/or discover new

  15. A Distributed Computational Architecture for Integrating Multiple Biomolecular Pathways

    E-print Network

    Ayyadurai, Shiva

    Biomolecular pathways are building blocks of cellular biochemical function. Computational biology is in rapid transition from diagrammatic representation of pathways to quantitative and predictive mathematical models, which ...

  16. Secretome analysis identifies novel signal Peptide peptidase-like 3 (sppl3) substrates and reveals a role of sppl3 in multiple Golgi glycosylation pathways.

    PubMed

    Kuhn, Peer-Hendrik; Voss, Matthias; Haug-Kröper, Martina; Schröder, Bernd; Schepers, Ute; Bräse, Stefan; Haass, Christian; Lichtenthaler, Stefan F; Fluhrer, Regina

    2015-06-01

    Signal peptide peptidase-like 3 (Sppl3) is a Golgi-resident intramembrane-cleaving protease that is highly conserved among multicellular eukaryotes pointing to pivotal physiological functions in the Golgi network which are only beginning to emerge. Recently, Sppl3 was shown to control protein N-glycosylation, when the key branching enzyme N-acetylglucosaminyltransferase V (GnT-V) and other medial/trans Golgi glycosyltransferases were identified as first physiological Sppl3 substrates. Sppl3-mediated endoproteolysis releases the catalytic ectodomains of these enzymes from their type II membrane anchors. Protein glycosylation is a multistep process involving numerous type II membrane-bound enzymes, but it remains unclear whether only few of them are Sppl3 substrates or whether Sppl3 cleaves many of them and thereby controls protein glycosylation at multiple levels. Therefore, to systematically identify Sppl3 substrates we used Sppl3-deficient and Sppl3-overexpression cell culture models and analyzed them for changes in secreted membrane protein ectodomains using the proteomics "secretome protein enrichment with click sugars (SPECS)" method. SPECS analysis identified numerous additional new Sppl3 candidate glycoprotein substrates, several of which were biochemically validated as Sppl3 substrates. All novel Sppl3 substrates adopt a type II topology. The majority localizes to the Golgi network and is implicated in Golgi functions. Importantly, most of the novel Sppl3 substrates catalyze the modification of N-linked glycans. Others contribute to O-glycan and in particular glycosaminoglycan biosynthesis, suggesting that Sppl3 function is not restricted to N-glycosylation, but also functions in other forms of protein glycosylation. Hence, Sppl3 emerges as a crucial player of Golgi function and the newly identified Sppl3 substrates will be instrumental to investigate the molecular mechanisms underlying the physiological function of Sppl3 in the Golgi network and in vivo. Data are available via ProteomeXchange with identifier PXD001672. PMID:25827571

  17. Evaluation of microbial triglyceride oil purification requirements for the CelTherm process: an efficient biochemical pathway to renewable fuels and chemicals.

    PubMed

    Linnen, Michael; Seames, Wayne; Kubatova, Alena; Menon, Suresh; Alisala, Kashinatham; Hash, Sara

    2014-10-01

    CelTherm is a biochemical process to produce renewable fuels and chemicals from lignocellulosic biomass. The present study's objective was to determine the level of treatment/purity of the microbial triacylglyceride oil (TAG) necessary to facilitate fuel production. After a unique microbe aerobically synthesizes TAG from biomass-derived sugars, the microbes were harvested and dried then crude TAG was chemically extracted from the residual biomass. Some TAGs were further purified to hydrotreating process requirements. Both grades were then noncatalytically cracked into a petroleum-like intermediate characterized by gas chromatography. Experiments were repeated using refined soybean oil for comparison to previous studies. The products from crude microbial TAG cracking were then further refined into a jet fuel product. Fuel tests indicate that this jet fuel corresponds to specifications for JP-8 military turbine fuel. It was thus concluded that the crude microbial TAG is a suitable feedstock with no further purification required, demonstrating CelTherm's commercial potential. PMID:24781206

  18. A network-based, integrative study to identify core biological pathways that drive breast cancer clinical subtypes

    PubMed Central

    Dutta, B; Pusztai, L; Qi, Y; André, F; Lazar, V; Bianchini, G; Ueno, N; Agarwal, R; Wang, B; Shiang, C Y; Hortobagyi, G N; Mills, G B; Symmans, W F; Balázsi, G

    2012-01-01

    Background: The rapid collection of diverse genome-scale data raises the urgent need to integrate and utilise these resources for biological discovery or biomedical applications. For example, diverse transcriptomic and gene copy number variation data are currently collected for various cancers, but relatively few current methods are capable to utilise the emerging information. Methods: We developed and tested a data-integration method to identify gene networks that drive the biology of breast cancer clinical subtypes. The method simultaneously overlays gene expression and gene copy number data on protein–protein interaction, transcriptional-regulatory and signalling networks by identifying coincident genomic and transcriptional disturbances in local network neighborhoods. Results: We identified distinct driver-networks for each of the three common clinical breast cancer subtypes: oestrogen receptor (ER)+, human epidermal growth factor receptor 2 (HER2)+, and triple receptor-negative breast cancers (TNBC) from patient and cell line data sets. Driver-networks inferred from independent datasets were significantly reproducible. We also confirmed the functional relevance of a subset of randomly selected driver-network members for TNBC in gene knockdown experiments in vitro. We found that TNBC driver-network members genes have increased functional specificity to TNBC cell lines and higher functional sensitivity compared with genes selected by differential expression alone. Conclusion: Clinical subtype-specific driver-networks identified through data integration are reproducible and functionally important. PMID:22343619

  19. Mutations in NMNAT1 cause Leber congenital amaurosis and identify a new disease pathway for retinal degeneration

    PubMed Central

    Koenekoop, Robert K.; Wang, Hui; Majewski, Jacek; Wang, Xia; Lopez, Irma; Ren, Huanan; Chen, Yiyun; Li, Yumei; Fishman, Gerald A.; Genead, Mohammed; Schwartzentruber, Jeremy; Solanki, Naimesh; Traboulsi, Elias I.; Cheng, Jingliang; Logan, Clare V.; McKibbin, Martin; Hayward, Bruce E.; Parry, David A.; Johnson, Colin A.; Nageeb, Mohammed; Poulter, James A.; Mohamed, Moin D.; Jafri, Hussain; Rashid, Yasmin; Taylor, Graham R.; Keser, Vafa; Mardon, Graeme; Xu, Huidan; Inglehearn, Chris F.; Fu, Qing; Toomes, Carmel; Chen, Rui

    2013-01-01

    Leber congenital amaurosis (LCA) is a blinding retinal disease that presents within the first year after birth. Using exome sequencing, we identified mutations in the nicotinamide adenine dinucleotide (NAD) synthase gene NMNAT1 encoding nicotinamide mononucleotide adenylyltransferase 1 in eight families with LCA, including the family in which LCA was originally linked to the LCA9 locus. Notably, all individuals with NMNAT1 mutations also have macular colobomas, which are severe degenerative entities of the central retina (fovea) devoid of tissue and photoreceptors. Functional assays of the proteins encoded by the mutant alleles identified in our study showed that the mutations reduce the enzymatic activity of NMNAT1 in NAD biosynthesis and affect protein folding. Of note, recent characterization of the slow Wallerian degeneration (Wlds) mouse model, in which prolonged axonal survival after injury is observed, identified NMNAT1 as a neuroprotective protein when ectopically expressed. Our findings identify a new disease mechanism underlying LCA and provide the first link between endogenous NMNAT1 dysfunction and a human nervous system disorder. PMID:22842230

  20. Supervised Model for Identifying Differentially Expressed Genes in DNA Microarray Gene Expression Dataset Using Biological Pathway Information

    Microsoft Academic Search

    Tae Su Chung; Keewon Kim; Ju Han Kim

    2005-01-01

    Microarray technology makes it possible to measure the expressions of tens of thousands of genes simultaneously under various experimental conditions. Identifying differentially expressed genes in each single experimental condition is one of the most common first steps in microarray gene expression data analysis. Reasonable choices of thresholds for determining differentially expressed genes are used for the next-step-analysis with suitable statistical

  1. Identification of biochemical pathways for the metabolism of oxidized low-density lipoprotein derived aldehyde-4-hydroxy trans-2-nonenal in vascular smooth muscle cells

    Microsoft Academic Search

    Sanjay Srivastava; Daniel J. Conklin; Si-Qi Liu; Nidhi Prakash; Paul J. Boor; Satish K. Srivastava; Aruni Bhatnagar

    2001-01-01

    Oxidation of low-density lipoproteins (LDL) generates high concentrations of unsaturated aldehydes, such as 4-hydroxy trans-2-nonenal (HNE). These aldehydes are mitogenic to vascular smooth muscle cells and sustain a vascular inflammation. Nevertheless, the processes that mediate and regulate the vascular metabolism of these aldehydes have not been examined. In this communication, we report the identification of the major metabolic pathways and

  2. Integrative analyses of miRNA and proteomics identify potential biological pathways associated with onset of pulmonary fibrosis in the bleomycin rat model.

    PubMed

    Fukunaga, Satoki; Kakehashi, Anna; Sumida, Kayo; Kushida, Masahiko; Asano, Hiroyuki; Gi, Min; Wanibuchi, Hideki

    2015-08-01

    To determine miRNAs and their predicted target proteins regulatory networks which are potentially involved in onset of pulmonary fibrosis in the bleomycin rat model, we conducted integrative miRNA microarray and iTRAQ-coupled LC-MS/MS proteomic analyses, and evaluated the significance of altered biological functions and pathways. We observed that alterations of miRNAs and proteins are associated with the early phase of bleomycin-induced pulmonary fibrosis, and identified potential target pairs by using ingenuity pathway analysis. Using the data set of these alterations, it was demonstrated that those miRNAs, in association with their predicted target proteins, are potentially involved in canonical pathways reflective of initial epithelial injury and fibrogenic processes, and biofunctions related to induction of cellular development, movement, growth, and proliferation. Prediction of activated functions suggested that lung cells acquire proliferative, migratory, and invasive capabilities, and resistance to cell death especially in the very early phase of bleomycin-induced pulmonary fibrosis. The present study will provide new insights for understanding the molecular pathogenesis of idiopathic pulmonary fibrosis. PMID:25933445

  3. Specific inhibitors for identifying pathways for methane production from carbon monoxide by a nonadapted anaerobic mixed culture.

    PubMed

    Navarro, Silvia Sancho; Cimpoia, Ruxandra; Bruant, Guillaume; Guiot, Serge R

    2014-06-01

    Specific inhibitors such as 2-bromoethanesulfonate (BES) and vancomycin were employed in activity batch tests to decipher metabolic pathways that are preferentially used by a mixed anaerobic consortium (sludge from an anaerobic digester) to transform carbon monoxide (CO) into methane (CH4). We first evaluated the inhibitory effect of both BES and vancomycin on the microbial community, as well as the efficiency and stability of vancomycin at 35 °C, over time. The activity tests with CO2-H2, CO, glucose, acetate, formate, propionate, butyrate, methanol, and ethanol showed that vancomycin does not inhibit some Gram-negative bacteria, and 50 mmol/L BES effectively blocks CH4 production in the sludge. However, when sludge was incubated with propionate, butyrate, methanol, or ethanol as the sole energy and carbon source, methanogenesis was only partially inhibited by BES. Separate tests showed that 0.07 mmol/L vancomycin is enough to maintain its inhibitory efficiency and stability in the population for at least 32 days at 35 °C. Using the inhibitors above, it was demonstrated that CO conversion to CH4 is an indirect, 2-step process, in which the CO is converted first to acetate and subsequently to CH4. PMID:24896194

  4. Pharmacological Inhibition of Nicotinamide Phosphoribosyltransferase/Visfatin Enzymatic Activity Identifies a New Inflammatory Pathway Linked to NAD

    PubMed Central

    Nobile, Massimo; Rolaz, Aline; Van Gool, Frédéric; Galli, Mara; Leo, Oberdan; So, Alexander; De Smedt, Thibaut

    2008-01-01

    Nicotinamide phosphoribosyltransferase (NAMPT), also known as visfatin, is the rate-limiting enzyme in the salvage pathway of NAD biosynthesis from nicotinamide. Since its expression is upregulated during inflammation, NAMPT represents a novel clinical biomarker in acute lung injury, rheumatoid arthritis, and Crohn's disease. However, its role in disease progression remains unknown. We report here that NAMPT is a key player in inflammatory arthritis. Increased expression of NAMPT was confirmed in mice with collagen-induced arthritis, both in serum and in the arthritic paw. Importantly, a specific competitive inhibitor of NAMPT effectively reduced arthritis severity with comparable activity to etanercept, and decreased pro-inflammatory cytokine secretion in affected joints. Moreover, NAMPT inhibition reduced intracellular NAD concentration in inflammatory cells and circulating TNF? levels during endotoxemia in mice. In vitro pharmacological inhibition of NAMPT reduced the intracellular concentration of NAD and pro-inflammatory cytokine secretion by inflammatory cells. Thus, NAMPT links NAD metabolism to inflammatory cytokine secretion by leukocytes, and its inhibition might therefore have therapeutic efficacy in immune-mediated inflammatory disorders. PMID:18493620

  5. Using genome-context data to identify specific types of functional associations in pathway\\/genome databases

    Microsoft Academic Search

    Michelle L. Green; Peter D. Karp

    2007-01-01

    Background: Hundreds of genes lacking homology to any protein of known function are sequenced every day. Genome-context methods have proved useful in providing clues about functional annotations for many proteins. However, genome-context methods detect many biological types of functional associations, and do not identify which type of functional association they have found. Results: We have developed two new genome-context-based algorithms.

  6. Parallel processing of afferent input by identified interneurones in the auditory pathway of the noctuid moth Noctua pronuba (L.)

    Microsoft Academic Search

    G. S. Boyan; Lee A. Miller

    1991-01-01

    1.Interneurones 501 and 504 are identified sound-sensitive interneurones in the pterothoracic ganglion of the noctuid moth Noctua pronuba (Fig. 1). Both neurones receive monosynaptic input from the A1 afferent (Figs. 2, 3) and experiments with current injection suggest that the synapse is chemical (Fig. 4). The EPSPs evoked in either IN 501 or 504 by the A1 afferent do not

  7. Identifying Resistance Mechanisms against Five Tyrosine Kinase Inhibitors Targeting the ERBB/RAS Pathway in 45 Cancer Cell Lines

    PubMed Central

    Szász, A. Marcell; Sztupinszki, Zsófia; Likó, István; Szendr?i, Attila; Schäfer, Reinhold; Gy?rffy, Balázs

    2013-01-01

    Because of the low overall response rates of 10–47% to targeted cancer therapeutics, there is an increasing need for predictive biomarkers. We aimed to identify genes predicting response to five already approved tyrosine kinase inhibitors. We tested 45 cancer cell lines for sensitivity to sunitinib, erlotinib, lapatinib, sorafenib and gefitinib at the clinically administered doses. A resistance matrix was determined, and gene expression profiles of the subsets of resistant vs. sensitive cell lines were compared. Triplicate gene expression signatures were obtained from the caArray project. Significance analysis of microarrays and rank products were applied for feature selection. Ninety-five genes were also measured by RT-PCR. In case of four sunitinib resistance associated genes, the results were validated in clinical samples by immunohistochemistry. A list of 63 top genes associated with resistance against the five tyrosine kinase inhibitors was identified. Quantitative RT-PCR analysis confirmed 45 of 63 genes identified by microarray analysis. Only two genes (ANXA3 and RAB25) were related to sensitivity against more than three inhibitors. The immunohistochemical analysis of sunitinib-treated metastatic renal cell carcinomas confirmed the correlation between RAB17, LGALS8, and EPCAM and overall survival. In summary, we determined predictive biomarkers for five tyrosine kinase inhibitors, and validated sunitinib resistance biomarkers by immunohistochemistry in an independent patient cohort. PMID:23555683

  8. A Genome-Wide Association Study of the Maize Hypersensitive Defense Response Identifies Genes That Cluster in Related Pathways

    PubMed Central

    Venkata, Bala P.; Marla, Sandeep; Ji, Jiabing; Gachomo, Emma; Chu, Kevin; Negeri, Adisu; Benson, Jacqueline; Nelson, Rebecca; Bradbury, Peter; Nielsen, Dahlia; Holland, James B.; Balint-Kurti, Peter J.; Johal, Gurmukh

    2014-01-01

    Much remains unknown of molecular events controlling the plant hypersensitive defense response (HR), a rapid localized cell death that limits pathogen spread and is mediated by resistance (R-) genes. Genetic control of the HR is hard to quantify due to its microscopic and rapid nature. Natural modifiers of the ectopic HR phenotype induced by an aberrant auto-active R-gene (Rp1-D21), were mapped in a population of 3,381 recombinant inbred lines from the maize nested association mapping population. Joint linkage analysis was conducted to identify 32 additive but no epistatic quantitative trait loci (QTL) using a linkage map based on more than 7000 single nucleotide polymorphisms (SNPs). Genome-wide association (GWA) analysis of 26.5 million SNPs was conducted after adjusting for background QTL. GWA identified associated SNPs that colocalized with 44 candidate genes. Thirty-six of these genes colocalized within 23 of the 32 QTL identified by joint linkage analysis. The candidate genes included genes predicted to be in involved programmed cell death, defense response, ubiquitination, redox homeostasis, autophagy, calcium signalling, lignin biosynthesis and cell wall modification. Twelve of the candidate genes showed significant differential expression between isogenic lines differing for the presence of Rp1-D21. Low but significant correlations between HR-related traits and several previously-measured disease resistance traits suggested that the genetic control of these traits was substantially, though not entirely, independent. This study provides the first system-wide analysis of natural variation that modulates the HR response in plants. PMID:25166276

  9. Structure/function analysis of a type iii polyketide synthase in the brown alga Ectocarpus siliculosus reveals a biochemical pathway in phlorotannin monomer biosynthesis.

    PubMed

    Meslet-Cladière, Laurence; Delage, Ludovic; Leroux, Cédric J-J; Goulitquer, Sophie; Leblanc, Catherine; Creis, Emeline; Gall, Erwan Ar; Stiger-Pouvreau, Valérie; Czjzek, Mirjam; Potin, Philippe

    2013-08-01

    Brown algal phlorotannins are structural analogs of condensed tannins in terrestrial plants and, like plant phenols, they have numerous biological functions. Despite their importance in brown algae, phlorotannin biosynthetic pathways have been poorly characterized at the molecular level. We found that a predicted type III polyketide synthase in the genome of the brown alga Ectocarpus siliculosus, PKS1, catalyzes a major step in the biosynthetic pathway of phlorotannins (i.e., the synthesis of phloroglucinol monomers from malonyl-CoA). The crystal structure of PKS1 at 2.85-Å resolution provided a good quality electron density map showing a modified Cys residue, likely connected to a long chain acyl group. An additional pocket not found in other known type III PKSs contains a reaction product that might correspond to a phloroglucinol precursor. In vivo, we also found a positive correlation between the phloroglucinol content and the PKS III gene expression level in cells of a strain of Ectocarpus adapted to freshwater during its reacclimation to seawater. The evolution of the type III PKS gene family in Stramenopiles suggests a lateral gene transfer event from an actinobacterium. PMID:23983220

  10. Pyrococcus furiosus flagella: biochemical and transcriptional analyses identify the newly detected flaB0 gene to encode the major flagellin.

    PubMed

    Näther-Schindler, Daniela J; Schopf, Simone; Bellack, Annett; Rachel, Reinhard; Wirth, Reinhard

    2014-01-01

    We have described previously that the flagella of the Euryarchaeon Pyrococcus furiosus are multifunctional cell appendages used for swimming, adhesion to surfaces and formation of cell-cell connections. Here, we characterize these organelles with respect to their biochemistry and transcription. Flagella were purified by shearing from cells followed by CsCl-gradient centrifugation and were found to consist mainly of a ca. 30 kDa glycoprotein. Polymerization studies of denatured flagella resulted in an ATP-independent formation of flagella-like filaments. The N-terminal sequence of the main flagellin was determined by Edman degradation, but none of the genes in the complete genome code for a protein with that N-terminus. Therefore, we resequenced the respective region of the genome, thereby discovering that the published genome sequence is not correct. A total of 771 bp are missing in the data base, resulting in the correction of the previously unusual N-terminal sequence of flagellin FlaB1 and in the identification of a third flagellin. To keep in line with the earlier nomenclature we call this flaB0. Very interestingly, the previously not identified flaB0 codes for the major flagellin. Transcriptional analyses of the revised flagellar operon identified various different cotranscripts encoding only a single protein in case of FlaB0 and FlaJ or up to five proteins (FlaB0-FlaD). Analysing the RNA of cells from different growth phases, we found that the length and number of detected cotranscript increased over time suggesting that the flagellar operon is transcribed mostly in late exponential and stationary growth phase. PMID:25566211

  11. Pyrococcus furiosus flagella: biochemical and transcriptional analyses identify the newly detected flaB0 gene to encode the major flagellin

    PubMed Central

    Näther-Schindler, Daniela J.; Schopf, Simone; Bellack, Annett; Rachel, Reinhard; Wirth, Reinhard

    2014-01-01

    We have described previously that the flagella of the Euryarchaeon Pyrococcus furiosus are multifunctional cell appendages used for swimming, adhesion to surfaces and formation of cell-cell connections. Here, we characterize these organelles with respect to their biochemistry and transcription. Flagella were purified by shearing from cells followed by CsCl-gradient centrifugation and were found to consist mainly of a ca. 30 kDa glycoprotein. Polymerization studies of denatured flagella resulted in an ATP-independent formation of flagella-like filaments. The N-terminal sequence of the main flagellin was determined by Edman degradation, but none of the genes in the complete genome code for a protein with that N-terminus. Therefore, we resequenced the respective region of the genome, thereby discovering that the published genome sequence is not correct. A total of 771 bp are missing in the data base, resulting in the correction of the previously unusual N-terminal sequence of flagellin FlaB1 and in the identification of a third flagellin. To keep in line with the earlier nomenclature we call this flaB0. Very interestingly, the previously not identified flaB0 codes for the major flagellin. Transcriptional analyses of the revised flagellar operon identified various different cotranscripts encoding only a single protein in case of FlaB0 and FlaJ or up to five proteins (FlaB0-FlaD). Analysing the RNA of cells from different growth phases, we found that the length and number of detected cotranscript increased over time suggesting that the flagellar operon is transcribed mostly in late exponential and stationary growth phase. PMID:25566211

  12. Integrating Bayesian variable selection with Modular Response Analysis to infer biochemical network topology

    PubMed Central

    2013-01-01

    Background Recent advancements in genetics and proteomics have led to the acquisition of large quantitative data sets. However, the use of these data to reverse engineer biochemical networks has remained a challenging problem. Many methods have been proposed to infer biochemical network topologies from different types of biological data. Here, we focus on unraveling network topologies from steady state responses of biochemical networks to successive experimental perturbations. Results We propose a computational algorithm which combines a deterministic network inference method termed Modular Response Analysis (MRA) and a statistical model selection algorithm called Bayesian Variable Selection, to infer functional interactions in cellular signaling pathways and gene regulatory networks. It can be used to identify interactions among individual molecules involved in a biochemical pathway or reveal how different functional modules of a biological network interact with each other to exchange information. In cases where not all network components are known, our method reveals functional interactions which are not direct but correspond to the interaction routes through unknown elements. Using computer simulated perturbation responses of signaling pathways and gene regulatory networks from the DREAM challenge, we demonstrate that the proposed method is robust against noise and scalable to large networks. We also show that our method can infer network topologies using incomplete perturbation datasets. Consequently, we have used this algorithm to explore the ERBB regulated G1/S transition pathway in certain breast cancer cells to understand the molecular mechanisms which cause these cells to become drug resistant. The algorithm successfully inferred many well characterized interactions of this pathway by analyzing experimentally obtained perturbation data. Additionally, it identified some molecular interactions which promote drug resistance in breast cancer cells. Conclusions The proposed algorithm provides a robust, scalable and cost effective solution for inferring network topologies from biological data. It can potentially be applied to explore novel pathways which play important roles in life threatening disease like cancer. PMID:23829771

  13. Large-scale association analyses identify new loci influencing glycemic traits and provide insight into the underlying biological pathways

    PubMed Central

    Scott, Robert A; Lagou, Vasiliki; Welch, Ryan P; Wheeler, Eleanor; Montasser, May E; Luan, Jian’an; Mägi, Reedik; Strawbridge, Rona J; Rehnberg, Emil; Gustafsson, Stefan; Kanoni, Stavroula; Rasmussen-Torvik, Laura J; Yengo, Loïc; Lecoeur, Cecile; Shungin, Dmitry; Sanna, Serena; Sidore, Carlo; Johnson, Paul C D; Jukema, J Wouter; Johnson, Toby; Mahajan, Anubha; Verweij, Niek; Thorleifsson, Gudmar; Hottenga, Jouke-Jan; Shah, Sonia; Smith, Albert V; Sennblad, Bengt; Gieger, Christian; Salo, Perttu; Perola, Markus; Timpson, Nicholas J; Evans, David M; Pourcain, Beate St; Wu, Ying; Andrews, Jeanette S; Hui, Jennie; Bielak, Lawrence F; Zhao, Wei; Horikoshi, Momoko; Navarro, Pau; Isaacs, Aaron; O’Connell, Jeffrey R; Stirrups, Kathleen; Vitart, Veronique; Hayward, Caroline; Esko, Tönu; Mihailov, Evelin; Fraser, Ross M; Fall, Tove; Voight, Benjamin F; Raychaudhuri, Soumya; Chen, Han; Lindgren, Cecilia M; Morris, Andrew P; Rayner, Nigel W; Robertson, Neil; Rybin, Denis; Liu, Ching-Ti; Beckmann, Jacques S; Willems, Sara M; Chines, Peter S; Jackson, Anne U; Kang, Hyun Min; Stringham, Heather M; Song, Kijoung; Tanaka, Toshiko; Peden, John F; Goel, Anuj; Hicks, Andrew A; An, Ping; Müller-Nurasyid, Martina; Franco-Cereceda, Anders; Folkersen, Lasse; Marullo, Letizia; Jansen, Hanneke; Oldehinkel, Albertine J; Bruinenberg, Marcel; Pankow, James S; North, Kari E; Forouhi, Nita G; Loos, Ruth J F; Edkins, Sarah; Varga, Tibor V; Hallmans, Göran; Oksa, Heikki; Antonella, Mulas; Nagaraja, Ramaiah; Trompet, Stella; Ford, Ian; Bakker, Stephan J L; Kong, Augustine; Kumari, Meena; Gigante, Bruna; Herder, Christian; Munroe, Patricia B; Caulfield, Mark; Antti, Jula; Mangino, Massimo; Small, Kerrin; Miljkovic, Iva; Liu, Yongmei; Atalay, Mustafa; Kiess, Wieland; James, Alan L; Rivadeneira, Fernando; Uitterlinden, Andre G; Palmer, Colin N A; Doney, Alex S F; Willemsen, Gonneke; Smit, Johannes H; Campbell, Susan; Polasek, Ozren; Bonnycastle, Lori L; Hercberg, Serge; Dimitriou, Maria; Bolton, Jennifer L; Fowkes, Gerard R; Kovacs, Peter; Lindström, Jaana; Zemunik, Tatijana; Bandinelli, Stefania; Wild, Sarah H; Basart, Hanneke V; Rathmann, Wolfgang; Grallert, Harald; Maerz, Winfried; Kleber, Marcus E; Boehm, Bernhard O; Peters, Annette; Pramstaller, Peter P; Province, Michael A; Borecki, Ingrid B; Hastie, Nicholas D; Rudan, Igor; Campbell, Harry; Watkins, Hugh; Farrall, Martin; Stumvoll, Michael; Ferrucci, Luigi; Waterworth, Dawn M; Bergman, Richard N; Collins, Francis S; Tuomilehto, Jaakko; Watanabe, Richard M; de Geus, Eco J C; Penninx, Brenda W; Hofman, Albert; Oostra, Ben A; Psaty, Bruce M; Vollenweider, Peter; Wilson, James F; Wright, Alan F; Hovingh, G Kees; Metspalu, Andres; Uusitupa, Matti; Magnusson, Patrik K E; Kyvik, Kirsten O; Kaprio, Jaakko; Price, Jackie F; Dedoussis, George V; Deloukas, Panos; Meneton, Pierre; Lind, Lars; Boehnke, Michael; Shuldiner, Alan R; van Duijn, Cornelia M; Morris, Andrew D; Toenjes, Anke; Peyser, Patricia A; Beilby, John P; Körner, Antje; Kuusisto, Johanna; Laakso, Markku; Bornstein, Stefan R; Schwarz, Peter E H; Lakka, Timo A; Rauramaa, Rainer; Adair, Linda S; Smith, George Davey; Spector, Tim D; Illig, Thomas; de Faire, Ulf; Hamsten, Anders; Gudnason, Vilmundur; Kivimaki, Mika; Hingorani, Aroon; Keinanen-Kiukaanniemi, Sirkka M; Saaristo, Timo E; Boomsma, Dorret I; Stefansson, Kari; van der Harst, Pim; Dupuis, Josée; Pedersen, Nancy L; Sattar, Naveed; Harris, Tamara B; Cucca, Francesco; Ripatti, Samuli; Salomaa, Veikko; Mohlke, Karen L; Balkau, Beverley; Froguel, Philippe; Pouta, Anneli; Jarvelin, Marjo-Riitta; Wareham, Nicholas J; Bouatia-Naji, Nabila; McCarthy, Mark I; Franks, Paul W; Meigs, James B; Teslovich, Tanya M; Florez, Jose C; Langenberg, Claudia; Ingelsson, Erik; Prokopenko, Inga; Barroso, Inês

    2012-01-01

    Through genome-wide association meta-analyses of up to 133,010 individuals of European ancestry without diabetes, including individuals newly genotyped using the Metabochip, we have raised the number of confirmed loci influencing glycemic traits to 53, of which 33 also increase type 2 diabetes risk (q < 0.05). Loci influencing fasting insulin showed association with lipid levels and fat distribution, suggesting impact on insulin resistance. Gene-based analyses identified further biologically plausible loci, suggesting that additional loci beyond those reaching genome-wide significance are likely to represent real associations. This conclusion is supported by an excess of directionally consistent and nominally significant signals between discovery and follow-up studies. Functional follow-up of these newly discovered loci will further improve our understanding of glycemic control. PMID:22885924

  14. Large-scale association analyses identify new loci influencing glycemic traits and provide insight into the underlying biological pathways.

    PubMed

    Scott, Robert A; Lagou, Vasiliki; Welch, Ryan P; Wheeler, Eleanor; Montasser, May E; Luan, Jian'an; Mägi, Reedik; Strawbridge, Rona J; Rehnberg, Emil; Gustafsson, Stefan; Kanoni, Stavroula; Rasmussen-Torvik, Laura J; Yengo, Loïc; Lecoeur, Cecile; Shungin, Dmitry; Sanna, Serena; Sidore, Carlo; Johnson, Paul C D; Jukema, J Wouter; Johnson, Toby; Mahajan, Anubha; Verweij, Niek; Thorleifsson, Gudmar; Hottenga, Jouke-Jan; Shah, Sonia; Smith, Albert V; Sennblad, Bengt; Gieger, Christian; Salo, Perttu; Perola, Markus; Timpson, Nicholas J; Evans, David M; Pourcain, Beate St; Wu, Ying; Andrews, Jeanette S; Hui, Jennie; Bielak, Lawrence F; Zhao, Wei; Horikoshi, Momoko; Navarro, Pau; Isaacs, Aaron; O'Connell, Jeffrey R; Stirrups, Kathleen; Vitart, Veronique; Hayward, Caroline; Esko, Tõnu; Mihailov, Evelin; Fraser, Ross M; Fall, Tove; Voight, Benjamin F; Raychaudhuri, Soumya; Chen, Han; Lindgren, Cecilia M; Morris, Andrew P; Rayner, Nigel W; Robertson, Neil; Rybin, Denis; Liu, Ching-Ti; Beckmann, Jacques S; Willems, Sara M; Chines, Peter S; Jackson, Anne U; Kang, Hyun Min; Stringham, Heather M; Song, Kijoung; Tanaka, Toshiko; Peden, John F; Goel, Anuj; Hicks, Andrew A; An, Ping; Müller-Nurasyid, Martina; Franco-Cereceda, Anders; Folkersen, Lasse; Marullo, Letizia; Jansen, Hanneke; Oldehinkel, Albertine J; Bruinenberg, Marcel; Pankow, James S; North, Kari E; Forouhi, Nita G; Loos, Ruth J F; Edkins, Sarah; Varga, Tibor V; Hallmans, Göran; Oksa, Heikki; Antonella, Mulas; Nagaraja, Ramaiah; Trompet, Stella; Ford, Ian; Bakker, Stephan J L; Kong, Augustine; Kumari, Meena; Gigante, Bruna; Herder, Christian; Munroe, Patricia B; Caulfield, Mark; Antti, Jula; Mangino, Massimo; Small, Kerrin; Miljkovic, Iva; Liu, Yongmei; Atalay, Mustafa; Kiess, Wieland; James, Alan L; Rivadeneira, Fernando; Uitterlinden, Andre G; Palmer, Colin N A; Doney, Alex S F; Willemsen, Gonneke; Smit, Johannes H; Campbell, Susan; Polasek, Ozren; Bonnycastle, Lori L; Hercberg, Serge; Dimitriou, Maria; Bolton, Jennifer L; Fowkes, Gerard R; Kovacs, Peter; Lindström, Jaana; Zemunik, Tatijana; Bandinelli, Stefania; Wild, Sarah H; Basart, Hanneke V; Rathmann, Wolfgang; Grallert, Harald; Maerz, Winfried; Kleber, Marcus E; Boehm, Bernhard O; Peters, Annette; Pramstaller, Peter P; Province, Michael A; Borecki, Ingrid B; Hastie, Nicholas D; Rudan, Igor; Campbell, Harry; Watkins, Hugh; Farrall, Martin; Stumvoll, Michael; Ferrucci, Luigi; Waterworth, Dawn M; Bergman, Richard N; Collins, Francis S; Tuomilehto, Jaakko; Watanabe, Richard M; de Geus, Eco J C; Penninx, Brenda W; Hofman, Albert; Oostra, Ben A; Psaty, Bruce M; Vollenweider, Peter; Wilson, James F; Wright, Alan F; Hovingh, G Kees; Metspalu, Andres; Uusitupa, Matti; Magnusson, Patrik K E; Kyvik, Kirsten O; Kaprio, Jaakko; Price, Jackie F; Dedoussis, George V; Deloukas, Panos; Meneton, Pierre; Lind, Lars; Boehnke, Michael; Shuldiner, Alan R; van Duijn, Cornelia M; Morris, Andrew D; Toenjes, Anke; Peyser, Patricia A; Beilby, John P; Körner, Antje; Kuusisto, Johanna; Laakso, Markku; Bornstein, Stefan R; Schwarz, Peter E H; Lakka, Timo A; Rauramaa, Rainer; Adair, Linda S; Smith, George Davey; Spector, Tim D; Illig, Thomas; de Faire, Ulf; Hamsten, Anders; Gudnason, Vilmundur; Kivimaki, Mika; Hingorani, Aroon; Keinanen-Kiukaanniemi, Sirkka M; Saaristo, Timo E; Boomsma, Dorret I; Stefansson, Kari; van der Harst, Pim; Dupuis, Josée; Pedersen, Nancy L; Sattar, Naveed; Harris, Tamara B; Cucca, Francesco; Ripatti, Samuli; Salomaa, Veikko; Mohlke, Karen L; Balkau, Beverley; Froguel, Philippe; Pouta, Anneli; Jarvelin, Marjo-Riitta; Wareham, Nicholas J; Bouatia-Naji, Nabila; McCarthy, Mark I; Franks, Paul W; Meigs, James B; Teslovich, Tanya M; Florez, Jose C; Langenberg, Claudia; Ingelsson, Erik; Prokopenko, Inga; Barroso, Inês

    2012-09-01

    Through genome-wide association meta-analyses of up to 133,010 individuals of European ancestry without diabetes, including individuals newly genotyped using the Metabochip, we have increased the number of confirmed loci influencing glycemic traits to 53, of which 33 also increase type 2 diabetes risk (q < 0.05). Loci influencing fasting insulin concentration showed association with lipid levels and fat distribution, suggesting impact on insulin resistance. Gene-based analyses identified further biologically plausible loci, suggesting that additional loci beyond those reaching genome-wide significance are likely to represent real associations. This conclusion is supported by an excess of directionally consistent and nominally significant signals between discovery and follow-up studies. Functional analysis of these newly discovered loci will further improve our understanding of glycemic control. PMID:22885924

  15. siRNA screening identifies differences in the Fanconi anemia pathway in BALB/c-Trp53+/? with susceptibility versus C57BL/6-Trp53+/? mice with resistance to mammary tumors

    PubMed Central

    Böhringer, M; Obermeier, K; Griner, N; Waldraff, D; Dickinson, E; Eirich, K; Schindler, D; Hagen, M; Jerry, D J; Wiesmüller, L

    2013-01-01

    BALB/c mice heterozygous for Trp53 develop a high proportion of spontaneous mammary tumors, a phenotype distinct from other mouse strains. BALB/c-Trp53+/? female mice, thus, resemble the hereditary Li-Fraumeni syndrome (LFS) characterized by early-onset of breast cancer, even though LFS involves TP53 mutations, which may involve not only loss- but also gain-of-function. Previous analysis of tumors in BALB/c-Trp53+/? females showed frequent loss of heterozygosity involving the wild-type allele of Trp53 and displayed characteristics indicative of mitotic recombination. Critical involvement of DNA double-strand break (DSB) repair dysfunction, particularly of homologous recombination (HR), was also noticed in the etiology of human breast cancer. To better define functional alterations in BALB/c-Trp53+/? mice, we applied a fluorescence-based DSB repair assay on mouse embryonic fibroblasts (MEFs) from BALB/c-Trp53+/? versus C57BL/6J-Trp53+/? mice. This approach revealed deregulation of HR but not non-homologous end-joining (NHEJ) in BALB/c-Trp53+/?, which was further confirmed for mammary epithelial cells. Screening of a small interfering RNA-library targeting DSB repair, recombination, replication and signaling genes, identified 25 genes causing differences between homologous DSB repair in the two strains upon silencing. Interactome analysis of the hits revealed clustering of replication-related and fanconi anemia (FA)/breast cancer susceptibility (BRCA) genes. Further dissection of the functional change in BALB/c-Trp53+/? by immunofluorescence microscopy of nuclear 53BP1, Replication protein A (RPA) and Rad51 foci uncovered differences in crosslink and replication-associated repair. Chromosome breakage, G2 arrest and biochemical analyses indicated a FA pathway defect downstream of FancD2 associated with reduced levels of BRCA2. Consistent with polygenic models for BRCA, mammary carcinogenesis in BALB/c-Trp53+/? mice may, therefore, be promoted by a BRCA modifier allele in the FA pathway in the context of partial p53 loss-of-function. PMID:23435420

  16. Genome-wide screen identifies a novel p97/CDC-48-dependent pathway regulating ER-stress-induced gene transcription.

    PubMed

    Marza, Esther; Taouji, Saïd; Barroso, Kim; Raymond, Anne-Aurélie; Guignard, Léo; Bonneu, Marc; Pallares-Lupon, Néstor; Dupuy, Jean-William; Fernandez-Zapico, Martin E; Rosenbaum, Jean; Palladino, Francesca; Dupuy, Denis; Chevet, Eric

    2015-03-01

    The accumulation of misfolded proteins in the endoplasmic reticulum (ER) activates the Unfolded Protein Response (UPR(ER)) to restore ER homeostasis. The AAA(+) ATPase p97/CDC-48 plays key roles in ER stress by promoting both ER protein degradation and transcription of UPR(ER) genes. Although the mechanisms associated with protein degradation are now well established, the molecular events involved in the regulation of gene transcription by p97/CDC-48 remain unclear. Using a reporter-based genome-wide RNAi screen in combination with quantitative proteomic analysis in Caenorhabditis elegans, we have identified RUVB-2, a AAA(+) ATPase, as a novel repressor of a subset of UPR(ER) genes. We show that degradation of RUVB-2 by CDC-48 enhances expression of ER stress response genes through an XBP1-dependent mechanism. The functional interplay between CDC-48 and RUVB-2 in controlling transcription of select UPR(ER) genes appears conserved in human cells. Together, these results describe a novel role for p97/CDC-48, whereby its role in protein degradation is integrated with its role in regulating expression of ER stress response genes. PMID:25652260

  17. Parallel processing of afferent input by identified interneurones in the auditory pathway of the noctuid moth Noctua pronuba (L.).

    PubMed

    Boyan, G S; Miller, L A

    1991-06-01

    1. Interneurones 501 and 504 are identified sound-sensitive interneurones in the pterothoracic ganglion of the noctuid moth Noctua pronuba. Both neurones receive monosynaptic input from the A1 afferent and experiments with current injection suggest that the synapse is chemical. The EPSPs evoked in either IN 501 or 504 by the A1 afferent do not facilitate. 2. Temporal integration in INs 501 and 504 was compared by presenting the moth with tones at repetition rates found in the search, approach and terminal phases of the echolocating call of a hunting bat. INs 501 and 504 differ in their capacity to resolve stimulus repetition rates because the mean decay times of their compound EPSPs differ by a factor of three, although both interneurones receive monosynaptic input from the A1 afferent. 3. The features extracted from the authentic, prerecorded, call of an echolocating bat at the level of the pterothoracic ganglion were examined by recording sequentially from a range of interneurones in the same preparation. The capacity of INs 501 and 504 to encode the various phases of the call was examined in the light of their measured mean decay times and related to the avoidance behaviour of the insect. PMID:1920166

  18. A System Biology Approach to Identify Regulatory Pathways Underlying the Neuroendocrine Control of Female Puberty in Rats and Nonhuman Primates

    PubMed Central

    Lomniczi, Alejandro; Wright, Hollis; Castellano, Juan Manuel; Sonmez, Kemal; Ojeda, Sergio R.

    2014-01-01

    Puberty is a major developmental milestone controlled by the interaction of genetic factors and environmental cues of mostly metabolic and circadian nature. An increased pulsatile release of the decapeptide gonadotropin releasing hormone (GnRH) from hypothalamic neurosecretory neurons is required for both the initiation and progression of the pubertal process. This increase is brought about by coordinated changes that occur in neuronal and glial networks associated with GnRH neurons. These changes ultimately result in increased neuronal and glial stimulatory inputs to the GnRH neuronal network and a reduction of transsynaptic inhibitory influences. While some of the major players controlling pubertal GnRH secretion have been identified using gene-centric approaches, much less is known about the system-wide control of the overall process. Because the pubertal activation of GnRH release involves a diversity of cellular phenotypes, and a myriad of intracellular and cell-to-cell signaling molecules, it appears that the overall process is controlled by a highly coordinated and interactive regulatory system involving hundreds, if not thousands, of gene products. In this article we will discuss emerging evidence suggesting that these genes are arranged as functionally connected networks organized, both internally and across sub-networks, in a hierarchical fashion. According to this concept, the core of these networks is composed of transcriptional regulators that, by directing expression of downstream subordinate genes, provide both stability and coordination to the cellular networks involved in initiating the pubertal process. The integrative response of these gene networks to external inputs is postulated to be coordinated by epigenetic mechanisms. PMID:23998662

  19. Time point-based integrative analyses of deep-transcriptome identify four signal pathways in blastemal regeneration of zebrafish lower jaw.

    PubMed

    Zhang, Hui; Wang, Xuelong; Lyu, Kailun; Gao, Siqi; Wang, Guan; Fan, Chunxin; Zhang, Xin A; Yan, Jizhou

    2015-03-01

    There has been growing interest in applying tissue engineering to stem cell-based regeneration therapies. We have previously reported that zebrafish can faithfully regenerate complicated tissue structures through blastemal cell type conversions and tissue reorganization. To unveil the regenerative factors and engineering arts of blastemal regeneration, we conducted transcriptomal analyses at four time points corresponding to preamputation, re-epitheliation, blastemal formation, and respecification. By combining the hierarchical gene ontology term network, the DAVID annotation system, and Euclidean distance clustering, we identified four signaling pathways: foxi1-foxo1b-pou3f1, pax3a-mant3a-col11/col2, pou5f1-cdx4-kdrl, and isl1-wnt11 PCP-sox9a. Results from immunohistochemical staining and promoter-driven transgenic fish suggest that these pathways, respectively, define wound epidermis reconstitution, cell type conversions, blastemal angiogenesis/vasculogenesis, and cartilage matrix-orientation. Foxi1 morpholino-knockdown caused expansions of Foxo1b- and Pax3a-expression in the basal layer-blastemal junction region. Moreover, foxi1 morphants displayed increased sox9a and hoxa2b transcripts in the embryonic pharyngeal arches. Thus, a Foxi1 signal switch is required to establish correct tissue patterns, including re-epitheliation and blastema formation. This study provides novel insight into a blastema regeneration strategy devised by epithelial cell transdifferentiation, blood vessel engineering, and cartilage matrix deposition. PMID:25420467

  20. Biochemical evidence on the potential role of organophosphates in hepatic glucose metabolism toward insulin resistance through inflammatory signaling and free radical pathways.

    PubMed

    Mostafalou, Sara; Eghbal, Mohammad Ali; Nili-Ahmadabadi, Amir; Baeeri, Maryam; Abdollahi, Mohammad

    2012-10-01

    Several studies show that organophosphate pesticides exert several effects on glucose homeostasis. The current study investigates the influence of subchronic exposure to malathion (MT) on hepatic gluconeogenesis in relation to acetyl cholinesterase (AChE) inhibition, oxidative stress and inflammatory response in the rat. MT was administered by gavage at doses of 25, 50 and 100 mg/kg for 32 days. Fasting hyperglycemia was seen in line with an increased activity of hepatic phosphoenolpyruvate carboxykinase, glucose 6-phosphatase and tumor necrosis factor ?. In addition to the impaired glucose tolerance and inhibition of AChE in a dose-dependent manner, there were significant increases in hepatic lipid peroxidation, carbonyl groups and 8-deoxyguanosine as the biomarkers of reactive oxygen species-mediated damage to lipid, protein and DNA, respectively. Altered quality of the liver in glucose production especially gluconeogenesis could be a compensatory mechanism against MT toxicity or even result in tissue damage. MT-induced insulin resistance in the liver occurs through oxidative and inflammatory signaling pathways. PMID:22082825

  1. Hyperoxia-Induced Protein Alterations in Renal Rat Tissue: A Quantitative Proteomic Approach to Identify Hyperoxia-Induced Effects in Cellular Signaling Pathways

    PubMed Central

    Hinkelbein, Jochen; Böhm, Lennert; Spelten, Oliver; Sander, David; Soltész, Stefan; Braunecker, Stefan

    2015-01-01

    Introduction. In renal tissue as well as in other organs, supranormal oxygen pressure may lead to deleterious consequences on a cellular level. Additionally, hyperoxia-induced effect in cells and related free radicals may potentially contribute to renal failure. The aim of this study was to analyze time-dependent alterations of rat kidney protein expression after short-term normobaric hyperoxia using proteomics and bioinformatic approaches. Material and Methods. N = 36 Wistar rats were randomized into six different groups: three groups with normobaric hyperoxia (exposure to 100% oxygen for 3?h) and three groups with normobaric normoxia (NN; room air). After hyperoxia exposure, kidneys were removed immediately, after 3 days and after 7 days. Kidney lysates were analyzed by two-dimensional gel electrophoresis followed by peptide mass fingerprinting using tandem mass spectrometry. Statistical analysis was performed with DeCyder 2D software (p < 0.01). Biological functions of differential regulated proteins were studied using functional network analysis (Ingenuity Pathways Analysis and PathwayStudio). Results. Expression of 14 proteins was significantly altered (p < 0.01): eight proteins (MEP1A_RAT, RSSA_RAT, F16P1_RAT, STML2_RAT, BPNT1_RAT, LGMN_RAT, ATPA_RAT, and VDAC1_RAT) were downregulated and six proteins (MTUS1_RAT, F16P1_RAT, ACTG_RAT, ACTB_RAT, 2ABA_RAT, and RAB1A_RAT) were upregulated. Bioinformatic analyses revealed an association of regulated proteins with inflammation. Conclusions. Significant alterations in renal protein expression could be demonstrated for up to 7 days even after short-term hyperoxia. The identified proteins indicate an association with inflammation signaling cascades. MEP1A and VDAC1 could be promising candidates to identify hyperoxic injury in kidney cells.

  2. BIOSYNTHETIC PATHWAYS: Biosynthesis Meets Bioinformatics

    NSDL National Science Digital Library

    David E. Cane (Brown University; Department of Chemistry)

    2000-02-04

    Access to the article is free, however registration and sign-in are required. In his Perspective, Cane discusses the increasing importance of the study of biosynthetic pathways in the discovery of biochemical reactions and pathways. Two recent papers (Rohdich et al. and Khaleeli et al.) highlight the increasing role of molecular biology and genomics in the study of biosynthetic pathways.

  3. Genome-scale RNAi on living-cell microarrays identifies novel regulators of Drosophila melanogaster TORC1–S6K pathway signaling

    PubMed Central

    Lindquist, Robert A.; Ottina, Kathleen A.; Wheeler, Douglas B.; Hsu, Peggy P.; Thoreen, Carson C.; Guertin, David A.; Ali, Siraj M.; Sengupta, Shomit; Shaul, Yoav D.; Lamprecht, Michael R.; Madden, Katherine L.; Papallo, Adam R.; Jones, Thouis R.; Sabatini, David M.; Carpenter, Anne E.

    2011-01-01

    The evolutionarily conserved target of rapamycin complex 1 (TORC1) controls cell growth in response to nutrient availability and growth factors. TORC1 signaling is hyperactive in cancer, and regulators of TORC1 signaling may represent therapeutic targets for human diseases. To identify novel regulators of TORC1 signaling, we performed a genome-scale RNA interference screen on microarrays of Drosophila melanogaster cells expressing human RPS6, a TORC1 effector whose phosphorylated form we detected by immunofluorescence. Our screen revealed that the TORC1–S6K–RPS6 signaling axis is regulated by many subcellular components, including the Class I vesicle coat (COPI), the spliceosome, the proteasome, the nuclear pore, and the translation initiation machinery. Using additional RNAi reagents, we confirmed 70 novel genes as significant on-target regulators of RPS6 phosphorylation, and we characterized them with extensive secondary assays probing various arms of the TORC1 pathways, identifying functional relationships among those genes. We conclude that cell-based microarrays are a useful platform for genome-scale and secondary screening in Drosophila, revealing regulators that may represent drug targets for cancers and other diseases of deregulated TORC1 signaling. PMID:21239477

  4. A genetic screen identifies TCF3/E2A and TRIAP1 as pathway-specific regulators of the cellular response to p53 activation

    PubMed Central

    Andrysik, Zdenek; Kim, Jihye; Tan, Aik Choon; Espinosa, Joaquín M.

    2013-01-01

    SUMMARY The p53 transcription factor participates in diverse cellular responses to stress including cell cycle arrest, apoptosis, senescence and autophagy. The molecular mechanisms defining the ultimate outcome to p53 activation remain poorly characterized. We performed a genome-wide genetic screen in human cells to identify pathway-specific coregulators of the p53 target genes CDKN1A (p21), an inhibitor of cell cycle progression, versus BBC3 (PUMA), a key mediator of apoptosis. Our screen identified numerous factors whose depletion creates an imbalance in the p21:PUMA ratio upon p53 activation. The transcription factor TCF3/E2A drives p21 expression while repressing PUMA across cancer cell types of multiple origins. Accordingly, TCF3/E2A depletion impairs the cell cycle arrest response and promotes apoptosis upon p53 activation by chemotherapeutic agents. In contrast, TRIAP1 is a specific repressor of p21 whose depletion slows down cell cycle progression. Our results reveal strategies to drive cells toward specific p53-dependent responses. PMID:23684607

  5. Integrated RNA-Seq and sRNA-Seq Analysis Identifies Chilling and Freezing Responsive Key Molecular Players and Pathways in Tea Plant (Camellia sinensis)

    PubMed Central

    Zheng, Chao; Zhao, Lei; Wang, Yu; Shen, Jiazhi; Zhang, Yinfei; Jia, Sisi; Li, Yusheng; Ding, Zhaotang

    2015-01-01

    Tea [Camellia sinensis (L) O. Kuntze, Theaceae] is one of the most popular non-alcoholic beverages worldwide. Cold stress is one of the most severe abiotic stresses that limit tea plants’ growth, survival and geographical distribution. However, the genetic regulatory network and signaling pathways involved in cold stress responses in tea plants remain unearthed. Using RNA-Seq, DGE and sRNA-Seq technologies, we performed an integrative analysis of miRNA and mRNA expression profiling and their regulatory network of tea plants under chilling (4?) and freezing (-5?) stress. Differentially expressed (DE) miRNA and mRNA profiles were obtained based on fold change analysis, miRNAs and target mRNAs were found to show both coherent and incoherent relationships in the regulatory network. Furthermore, we compared several key pathways (e.g., ‘Photosynthesis’), GO terms (e.g., ‘response to karrikin’) and transcriptional factors (TFs, e.g., DREB1b/CBF1) which were identified as involved in the early chilling and/or freezing response of tea plants. Intriguingly, we found that karrikins, a new group of plant growth regulators, and ?-primeverosidase (BPR), a key enzyme functionally relevant with the formation of tea aroma might play an important role in both early chilling and freezing response of tea plants. Quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) analysis further confirmed the results from RNA-Seq and sRNA-Seq analysis. This is the first study to simultaneously profile the expression patterns of both miRNAs and mRNAs on a genome-wide scale to elucidate the molecular mechanisms of early responses of tea plants to cold stress. In addition to gaining a deeper insight into the cold resistant characteristics of tea plants, we provide a good case study to analyse mRNA/miRNA expression and profiling of non-model plant species using next-generation sequencing technology. PMID:25901577

  6. A Fluorescent Live Imaging Screening Assay Based on Translocation Criteria Identifies Novel Cytoplasmic Proteins Implicated in G Protein-coupled Receptor Signaling Pathways.

    PubMed

    Lecat, Sandra; Matthes, Hans W D; Pepperkok, Rainer; Simpson, Jeremy C; Galzi, Jean-Luc

    2015-05-01

    Several cytoplasmic proteins that are involved in G protein-coupled receptor signaling cascades are known to translocate to the plasma membrane upon receptor activation, such as beta-arrestin2. Based on this example and in order to identify new cytoplasmic proteins implicated in the ON-and-OFF cycle of G protein-coupled receptor, a live-imaging screen of fluorescently labeled cytoplasmic proteins was performed using translocation criteria. The screening of 193 fluorescently tagged human proteins identified eight proteins that responded to activation of the tachykinin NK2 receptor by a change in their intracellular localization. Previously we have presented the functional characterization of one of these proteins, REDD1, that translocates to the plasma membrane. Here we report the results of the entire screening. The process of cell activation was recorded on videos at different time points and all the videos can be visualized on a dedicated website. The proteins BAIAP3 and BIN1, partially translocated to the plasma membrane upon activation of NK2 receptors. Proteins ARHGAP12 and PKM2 translocated toward membrane blebs. Three proteins that associate with the cytoskeleton were of particular interest : PLEKHH2 rearranged from individual dots located near the cell-substrate adhesion surface into lines of dots. The speriolin-like protein, SPATC1L, redistributed to cell-cell junctions. The Chloride intracellular Channel protein, CLIC2, translocated from actin-enriched plasma membrane bundles to cell-cell junctions upon activation of NK2 receptors. CLIC2, and one of its close paralogs, CLIC4, were further shown to respond with the same translocation pattern to muscarinic M3 and lysophosphatidic LPA receptors. This screen allowed us to identify potential actors in signaling pathways downstream of G protein-coupled receptors and could be scaled-up for high-content screening. PMID:25759509

  7. Enumerating Minimal Active Metabolic Pathways by Model Generation

    NASA Astrophysics Data System (ADS)

    Soh, Takehide; Inoue, Katsumi

    In systems biology, identifying vital functions like glycolysis from a given metabolic pathway is important to understand living organisms. In this paper, we particularly focus on the problem of enumerating minimal active pathways producing target metabolites from source metabolites. We represent the problem in propositional formulas and solve it through minimal model generation. An advantage of our method is that each solution satisfies qualitative laws of biochemical reactions. Moreover, we can calculate such solutions for a cellular scale metabolic pathway within a few seconds. In experiments, we have applied our method to a whole Escherichia coli metabolic pathway. As a result, we found a minimal set of reactions corresponding to the conventional glycolysis pathway described in a biological database EcoCyc.

  8. Genomic and Biochemical Analysis of the Diaminopimelate and Lysine Biosynthesis Pathway in Verrucomicrobium spinosum: Identification and Partial Characterization of L,L-Diaminopimelate Aminotransferase and UDP-N-Acetylmuramoylalanyl-D-glutamyl-2,6-meso-Diaminopimelate Ligase

    PubMed Central

    Nachar, Victoria R.; Savka, Francisco C.; McGroty, Sean E.; Donovan, Katherine A.; North, Rachel A.; Dobson, Renwick C. J.; Buckley, Larry J.; Hudson, André O.

    2012-01-01

    The Gram-negative bacterium Verrucomicrobium spinosum has attracted interest in recent years following the sequencing and annotation of its genome. Comparative genomic analysis of V. spinosum using diaminopimelate/lysine metabolic genes from Chlamydia trachomatis suggests that V. spinosum employs the L,L-diaminopimelate aminotransferase (DapL) pathway for diaminopimelate/lysine biosynthesis. The open reading frame corresponding to the putative dapL ortholog was cloned and the recombinant enzyme was shown to possess L,L-diaminopimelate aminotransferase activity in vitro. In vivo analysis using functional complementation confirmed that the dapL ortholog was able to functionally complement an E. coli mutant that confers auxotrophy for diaminopimelate and lysine. In addition to its role in lysine biosynthesis, the intermediate diaminopimelate has an integral role in peptidoglycan biosynthesis. To this end, the UDP-N-acetylmuramoylalanyl-d-glutamyl-2,6-meso-diaminopimelate ligase ortholog was also identified, cloned, and was shown to possess meso-diaminopimelate ligase activity in vivo. The L,L-diaminopimelate aminotransferase pathway has been experimentally confirmed in several bacteria, some of which are deemed pathogenic to animals. Since animals, and particularly humans, lack the genetic machinery for the synthesis of diaminopimelate/lysine de novo, the enzymes involved in this pathway are attractive targets for development of antibiotics. Whether dapL is an essential gene in any bacteria is currently not known. V. spinosum is an excellent candidate to investigate the essentiality of dapL, since the bacterium employs the DapL pathway for lysine and cell wall biosynthesis, is non-pathogenic to humans, facile to grow, and can be genetically manipulated. PMID:22783236

  9. Next-generation sequencing of salivary high-grade neuroendocrine carcinomas identifies alterations in RB1 and the mTOR pathway.

    PubMed

    Goyal, Bella; Duncavage, Eric J; Martinez, David; Lewis, James S; Chernock, Rebecca D

    2014-12-01

    Salivary gland high-grade neuroendocrine carcinomas are rare, aggressive tumors that are morphologically and immunohistochemically similar to cutaneous high-grade neuroendocrine (Merkel cell) carcinomas. The majority of Merkel cell carcinomas harbor Merkel cell polyomavirus, while the virus is rare or absent in salivary high-grade neuroendocrine carcinomas. Inactivation of retinoblastoma 1 (RB1) has been implicated in the pathogenesis of both virus-positive and -negative Merkel cell carcinomas but by different mechanisms. In virus-positive tumors, a portion of the viral genome, the large T antigen, may inactivate RB1, and in virus-negative Merkel cell carcinomas truncating mutations in the RB1 gene have been identified. The molecular genetics of salivary high-grade neuroendocrine carcinomas are not well understood. Here, we performed targeted next-generation sequencing of 151 cancer-related genes on 4 four Merkel cell polyomavirus-negative primary salivary gland high-grade neuroendocrine carcinoma cases. Somatic mutations were predominantly found within tumor suppressor genes [TP53 (3 cases), PTEN (2 cases), RB1 (1 case)]. Truncating RB1 mutations, as seen in virus-negative Merkel cell carcinomas, were not identified. However, 3 of 4 cases had RB1 deletions by copy number variation analysis. The 4th case had loss of heterozygosity for RB1. Fluorescence in situ hybridization confirmed RB1 deletions in 2 of 3 cases, and the absence of RB1 deletion in the 4th case that had loss of heterozygosity. All 4 cases showed loss of RB1 protein expression by immunohistochemistry, indicating that RB1 inactivation is important. However, the mechanism of RB1 inactivation appears different than that seen in Merkel cell carcinomas. In addition, copy number variation consistent with activation of the PI3KCA/AKT/mTOR pathway was also observed in all 4 cases. The mTOR pathway may be a potential therapeutic target in these tumors as mTOR inhibitors are currently used to treat other tumor types. PMID:25446844

  10. Genome-wide association study for colorectal cancer identifies risk polymorphisms in German familial cases and implicates MAPK signalling pathways in disease susceptibility.

    PubMed

    Lascorz, Jesús; Försti, Asta; Chen, Bowang; Buch, Stephan; Steinke, Verena; Rahner, Nils; Holinski-Feder, Elke; Morak, Monika; Schackert, Hans K; Görgens, Heike; Schulmann, Karsten; Goecke, Timm; Kloor, Matthias; Engel, Cristoph; Büttner, Reinhard; Kunkel, Nelli; Weires, Marianne; Hoffmeister, Michael; Pardini, Barbara; Naccarati, Alessio; Vodickova, Ludmila; Novotny, Jan; Schreiber, Stefan; Krawczak, Michael; Bröring, Clemens D; Völzke, Henry; Schafmayer, Clemens; Vodicka, Pavel; Chang-Claude, Jenny; Brenner, Hermann; Burwinkel, Barbara; Propping, Peter; Hampe, Jochen; Hemminki, Kari

    2010-09-01

    Genetic susceptibility accounts for approximately 35% of all colorectal cancer (CRC). Ten common low-risk variants contributing to CRC risk have been identified through genome-wide association studies (GWASs). In our GWAS, 610 664 genotyped single-nucleotide polymorphisms (SNPs) passed the quality control filtering in 371 German familial CRC patients and 1263 controls, and replication studies were conducted in four additional case-control sets (4915 cases and 5607 controls). Known risk loci at 8q24.21 and 11q23 were confirmed, and a previously unreported association, rs12701937, located between the genes GLI3 (GLI family zinc finger 3) and INHBA (inhibin, beta A) [P = 1.1 x 10(-3), odds ratio (OR) 1.14, 95% confidence interval (CI) 1.05-1.23, dominant model in the combined cohort], was identified. The association was stronger in familial cases compared with unselected cases (P = 2.0 x 10(-4), OR 1.36, 95% CI 1.16-1.60, dominant model). Two other unreported SNPs, rs6038071, 40 kb upstream of CSNK2A1 (casein kinase 2, alpha 1 polypeptide) and an intronic marker in MYO3A (myosin IIIA), rs11014993, associated with CRC only in the familial CRC cases (P = 2.5 x 10(-3), recessive model, and P = 2.7 x 10(-4), dominant model). Three software tools successfully pointed to the overrepresentation of genes related to the mitogen-activated protein kinase (MAPK) signalling pathways among the 1340 most strongly associated markers from the GWAS (allelic P value < 10(-3)). The risk of CRC increased significantly with an increasing number of risk alleles in seven genes involved in MAPK signalling events (P(trend) = 2.2 x 10(-16), OR(per allele) = 1.34, 95% CI 1.11-1.61). PMID:20610541

  11. ChIP-Seq and RNA-Seq Analyses Identify Components of the Wnt and Fgf Signaling Pathways as Prep1 Target Genes in Mouse Embryonic Stem Cells

    PubMed Central

    Laurent, Audrey; Calabrese, Manuela; Warnatz, Hans-Jörg; Yaspo, Marie-Laure; Tkachuk, Vsevolod; Torres, Miguel; Blasi, Francesco; Penkov, Dmitry

    2015-01-01

    The Prep1 (Pknox1) homeodomain transcription factor is essential at multiple stages of embryo development. In the E11.5 embryo trunk, we previously estimated that Prep1 binds about 3,300 genomic sites at a highly specific decameric consensus sequence, mainly governing basal cellular functions. We now show that in embryonic stem (ES) cells Prep1 binding pattern only partly overlaps that of the embryo trunk, with about 2,000 novel sites. Moreover, in ES cells Prep1 still binds mostly to promoters, as in total embryo trunk but, among the peaks bound exclusively in ES cells, the percentage of enhancers was three-fold higher. RNA-seq identifies about 1800 genes down-regulated in Prep1-/- ES cells which belong to gene ontology categories not enriched in the E11.5 Prep1i/i differentiated embryo, including in particular essential components of the Wnt and Fgf pathways. These data agree with aberrant Wnt and Fgf expression levels in the Prep1-/- ES cells with a deficient embryoid bodies (EBs) formation and differentiation. Re-establishment of the Prep1 level rescues the phenotype. PMID:25875616

  12. Biochemical genetic markers in sugarcane

    Microsoft Academic Search

    J. C. Glaszmann; A. Fautret; J. L. Noyer; P. Feldmann; C. Lanaud

    1989-01-01

    Isozyme variation was used to identify biochemical markers of potential utility in sugarcane genetics and breeding. Electrophoretic polymorphism was surveyed for nine enzymes among 39 wild and noble sugarcane clones, belonging to the species most closely related to modern varieties. Up to 114 distinct bands showing presence versus absence type of variation were revealed and used for qualitative characterization of

  13. An Inductive Logic Programming Approach to Validate Hexose Binding Biochemical Knowledge

    E-print Network

    Page Jr., C. David

    of Computer Sciences, 2 Department of Biostatistics and Medical Informatics, University of Wisconsin simple sugar molecules that play a key role in different biochemical pathways, including cellular energy

  14. Regulation of biochemical pathways involved in neurodegeneration

    E-print Network

    Pooler, Amy Melissa

    2005-01-01

    Alzheimer's disease (AD) is a neurodegenerative disorder characterized by cognitive decline and memory loss. Although much is known about how AD affects the brain, the cause of this disease remains elusive. Current AD ...

  15. A combined remote sensing and modeling based approach to identify sustainable pathways for urban and peri-urban agriculture in China

    NASA Astrophysics Data System (ADS)

    Wattenbach, M.; Delgado, J. M.; Roessner, S.; Bochow, M.; Güntner, A.; Kropp, J.; Cantu Ros, A. G.; Hattermann, F.; Kolbe, T.; Sodoudi, S.; Cubasch, U. Ulrich; Zeitz, J.; Ross, L.; Böckel, K.; Fang, C.; Bo, L.; Pan, G.

    2012-04-01

    As the world's biggest economy, China is becoming the biggest consumer of resources globally. Given this trend, the over-proportional fast increase in urbanization presents China with fundamental problems. Among the most urgent ones is the increasing loss of agricultural land as urbanization takes place in the most productive regions along the coast. The latter is being responsible for a shift in agriculture production towards climatically less favorable areas. At the same time, the loss of green areas in and around growing cities is increasing the effect of the urban heat island. The perception of the potential risks related to this phenomenon, in the context of climate change, has led the Shanghai city administration to increase its urban-greening efforts, expanding the per capita area of green from 1m2 in 1990 to 12.5m2 in 2008. In this context, this paper aims at identifying the influence of urban and peri-urban agriculture (UPA) on the sustainability of the urban regions of Shanghai and Nanjing. In particular, it focuses on the effects of UPA on the greenhouse gas (GHG) emissions, soil nutrients and water balances, local climate and the structure and functions of the urbanized areas. We propose an interdisciplinary framework combining remote sensing, model simulations and GHG field observations and targeted at identifying "win-win" strategies for sustainable planning pathways showing high potentials for UPA. The framework is based on spatial scenario modeling, automatic classification of urban structure types and on a prototype of a high-quality spatial database consisting of a 3D city model. Dynamic boundary conditions for climate and urban development are provided by state of the art models. These approaches meet the needs of stakeholders and planners in China. A special emphasis is put on interdependencies between small holder farming in the urban and peri-urban zone and climate change adaptation and mitigation strategies focusing on improved management of local water and nutrient cycles. The whole database generated will be structured and made accessible for planners and stakeholders in the form of a 3D city visualization model.

  16. CSNK1A1 and Gli2 as Novel Targets Identified Through an Integrative Analysis of Gene Expression Data, Protein-Protein Interaction and Pathways Networks in Glioblastoma Tumors: Can These Two Be Antagonistic Proteins?

    PubMed Central

    Mishra, Seema

    2014-01-01

    Glioblastoma (GBM) is the malignant form of glioma, and the interplay of different pathways working in concert in GBM development and progression needs to be fully understood. Wnt signaling and sonic hedgehog (SHH) signaling pathways, having basic similarities, are among the major pathways aberrantly activated in GBM, and hence, need to be targeted. It becomes imperative, therefore, to explore the functioning of these pathways in context of each other in GBM. An integrative approach may help provide new biological insights, as well as solve the problem of identifying common drug targets for simultaneous targeting of these pathways. The beauty of this approach is that it can recapitulate several known facts, as well as decipher new emerging patterns, identifying those targets that could be missed when relying on one type of data at a time. This approach can be easily extended to other systems to discover key patterns in the functioning of signaling molecules. Studies were designed to assess the relationship between significant differential expression of genes of the Wnt (Wnt/?-catenin canonical and Wnt non-canonical) and SHH signaling pathways and their connectivity patterns in interaction and signaling networks. Further, the aim was to decipher underlying mechanistic patterns that may be involved in a more specific way and to generate a ranked list of genes that can be used as markers or drug targets. These studies predict that Wnt pathway plays a relatively more pro-active role than the SHH pathway in GBM. Further, CTNNB1, CSNK1A1, and Gli2 proteins may act as key drug targets common to these pathways. While CTNNB1 is a widely studied molecule in the context of GBM, the likely roles of CSNK1A1 and Gli2 are found to be relatively novel. It is surmised that Gli2 may be antagonistic to CSNK1A1, preventing the phosphorylation of CTNNB1 and SMO proteins in Wnt and SHH signaling pathway, respectively, by CSNK1A1, and thereby, aberrant activation. New insights into the possible behavior of these pathway molecules relative to each other in GBM reveal some key interesting patterns. PMID:25374452

  17. PathMiner: predicting metabolic pathways by heuristic search

    PubMed Central

    McShan, D.C.; Rao, S.; Shah, I.

    2009-01-01

    Motivation Automated methods for biochemical pathway inference are becoming increasingly important for understanding biological processes in living and synthetic systems. With the availability of data on complete genomes and increasing information about enzyme-catalyzed biochemistry it is becoming feasible to approach this problem computationally. In this paper we present PathMiner, a system for automatic metabolic pathway inference. PathMiner predicts metabolic routes by reasoning over transformations using chemical and biological information. Results We build a biochemical state-space using data from known enzyme-catalyzed transformations in Ligand, including, 2917 unique transformations between 3890 different compounds. To predict metabolic pathways we explore this state-space by developing an informed search algorithm. For this purpose we develop a chemically motivated heuristic to guide the search. Since the algorithm does not depend on predefined pathways, it can efficiently identify plausible routes using known biochemical transformations. Contact imran.shah@uchsc.edu Availability The system is available for testing at http://pathminer.uchsc.edu PMID:12967966

  18. A Global Genomic and Genetic Strategy to Identify, Validate and Use Gene Signatures of Xenobiotic-Responsive Transcription Factors in Prediction of Pathway Activation in the Mouse Liver

    EPA Science Inventory

    Many drugs and environmentally-relevant chemicals activate xenobiotic-responsive transcription factors. Identification of target genes of these factors would be useful in predicting pathway activation in in vitro chemical screening as well as their involvement in disease states. ...

  19. IL1  mediated up-regulation of HIF-1  via an NFkB\\/COX2 pathway identifies HIF-1 as a critical link between inflammation and oncogenesis

    Microsoft Academic Search

    Yun-Jin Jung; Jennifer S. Isaacs; Sunmin Lee; Jane Trepel; Len Neckers

    2003-01-01

    Growing evidence indicates that inflammation is a contributing factor leading to cancer development. However, pathways involved in this progression are not well understood. To examine whether HIF-1? is a factor linking inflammation and tumorigenesis, we investigated whether the HIF-1 signaling pathway was stimulated by the pro-inflammatory cytokine interleukin-1? (IL-1?) in A549 cells. We find that IL-1? up-regulated HIF-1? protein under

  20. Fe-S Cluster Assembly Pathways in Bacteria

    PubMed Central

    Ayala-Castro, Carla; Saini, Avneesh; Outten, F. Wayne

    2008-01-01

    Summary: Iron-sulfur (Fe-S) clusters are required for critical biochemical pathways, including respiration, photosynthesis, and nitrogen fixation. Assembly of these iron cofactors is a carefully controlled process in cells to avoid toxicity from free iron and sulfide. Multiple Fe-S cluster assembly pathways are present in bacteria to carry out basal cluster assembly, stress-responsive cluster assembly, and enzyme-specific cluster assembly. Although biochemical and genetic characterization is providing a partial picture of in vivo Fe-S cluster assembly, a number of mechanistic questions remain unanswered. Furthermore, new factors involved in Fe-S cluster assembly and repair have recently been identified and are expanding the complexity of current models. Here we attempt to summarize recent advances and to highlight new avenues of research in the field of Fe-S cluster assembly. PMID:18322036

  1. Applying meta-pathway analyses through metagenomics to identify the functional properties of the major bacterial communities of a single spontaneous cocoa bean fermentation process sample.

    PubMed

    Illeghems, Koen; Weckx, Stefan; De Vuyst, Luc

    2015-09-01

    A high-resolution functional metagenomic analysis of a representative single sample of a Brazilian spontaneous cocoa bean fermentation process was carried out to gain insight into its bacterial community functioning. By reconstruction of microbial meta-pathways based on metagenomic data, the current knowledge about the metabolic capabilities of bacterial members involved in the cocoa bean fermentation ecosystem was extended. Functional meta-pathway analysis revealed the distribution of the metabolic pathways between the bacterial members involved. The metabolic capabilities of the lactic acid bacteria present were most associated with the heterolactic fermentation and citrate assimilation pathways. The role of Enterobacteriaceae in the conversion of substrates was shown through the use of the mixed-acid fermentation and methylglyoxal detoxification pathways. Furthermore, several other potential functional roles for Enterobacteriaceae were indicated, such as pectinolysis and citrate assimilation. Concerning acetic acid bacteria, metabolic pathways were partially reconstructed, in particular those related to responses toward stress, explaining their metabolic activities during cocoa bean fermentation processes. Further, the in-depth metagenomic analysis unveiled functionalities involved in bacterial competitiveness, such as the occurrence of CRISPRs and potential bacteriocin production. Finally, comparative analysis of the metagenomic data with bacterial genomes of cocoa bean fermentation isolates revealed the applicability of the selected strains as functional starter cultures. PMID:25998815

  2. Thermodynamic analysis of trinitrotoluene biodegradation and mineralization pathways

    SciTech Connect

    Shelley, M.D.; Autenrieth, R.L.; Wild, J.R.; Dale, B.E. [Texas A and M Univ., College Station, TX (United States)] [Texas A and M Univ., College Station, TX (United States)

    1996-07-20

    Biodegradation of 2,4,6-trinitrotoluene (TNT) proceeds through several different metabolic pathways. However, the reaction steps which are considered rate-controlling have not been fully determined. Glycolysis and other biological pathways contain biochemical reactions which are acutely rate-limiting due to enzyme control. These rate-limiting steps also have large negative Gibbs free energy changes. Because xenobiotic compounds such as TNT can be used by biological systems as nitrogen, carbon, and energy sources, it is likely that their degradation pathways also contain acutely rate-limiting steps. Identification of these rate-controlling reactions will enhance and better direct genetic engineering techniques to increase specific enzyme levels. This article identifies likely rate-controlling steps (or sets of steps) in reported TNT biodegradation pathways by estimating the Gibbs free energy change for each step and for the overall pathways. The biological standard Gibbs free energy change of reaction was calculated for each pathway step using a group contribution method specifically tailored for biomolecules. The method was also applied to hypothetical pathways constructed to mineralize TNT using several different microorganisms. Pathways steps that have large negative Gibbs free energy changes are postulated to be potentially rate-controlling. The microorganisms which utilize degradation pathways with the largest overall (from TNT to citrate) negative Gibbs free energy changes were also determined.

  3. Exchange reactions catalyzed by group-transferring enzymes oppose the quantitation and the unravelling of the identify of the pentose pathway.

    PubMed

    Flanigan, I; Collins, J G; Arora, K K; MacLeod, J K; Williams, J F

    1993-04-01

    1. The distributions and rates of transfer of carbon isotopes from a selection of specifically labelled ketosugar-phosphate substrates by exchange reactions catalyzed by the pentose and photosynthetic carbon-reduction-pathway group-transferring enzymes transketolase, transaldolase and aldolase have been measured using 13C-NMR spectroscopy. 2. The rates of these exchange reactions were 5, 4 and 1.5 mumol min-1 mg-1 for transketolase exchange, transaldolase exchange and aldolase exchange, respectively. 3. A comparison of the exchange capacities contributed by the activities of these enzymes in three in vitro liver preparations with the maximum non-oxidative pentose pathway flux rates of the preparations shows that transketolase and aldolase exchanges exceeded flux by 9-19 times in liver cytosol and acetone powder enzyme preparations and by 5 times in hepatocytes. Transaldolase was less effective in the comparison of exchange versus flux rates: transaldolase exchange exceeded flux by 1.6 and 5 in catalysis by liver cytosol and acetone powder preparations, respectively, but was only 0.6 times the flux in hepatocytes. 4. Values of group enzyme exchange and pathway flux rates in the above three preparations are important because of the feature role of liver and of these particular preparations in the establishment, elucidation and measurement of a proposed reaction scheme for the fat-cell-type pentose pathway in biochemistry. 5. It is the claim of this paper that the excess of exchange rate activity (particularly transketolase exchange) over pathway flux will overturn attempts to unravel, using isotopically labelled sugar substrates, the identity, reaction sequence and quantitative contribution of the pentose pathway to glucose metabolism. 6. The transketolase exchange reactions relative to the pentose pathway flux rates in normal, regenerating and foetal liver, Morris hepatomas, mammary carcinoma, melanoma, colonic epithelium, spinach chloroplasts and epididymal fat tissue show that transketolase exchange may exceed flux in these tissues by factors ranging over 5-600 times. 7. The confusion of pentose pathway theory by the effects of transketolase exchange action is illustrated by the 13C-NMR spectrum of the hexose 6-phosphate products of ribose 5-phosphate dissimilation, formed after 30 min of liver enzyme action, and shows 13C-labelling in carbons 1 and 3 of glucose 6-phosphate with ratios which range over 2.1-6.4 rather than the mandatory value of 2 which is imposed by the theoretical mechanism of the pathway. PMID:8477719

  4. Heterologous protein production using the twin arginine translocation pathway

    DOEpatents

    Pohlschroder, Mechtild (Philadelphia, PA); Kissinger, Jessica C (Athens, GA); Rose, R. Wesley (Glenside, PA); Brueser, Thomas (Halle, DE); Dilks, Kieran (Collingswood, NJ)

    2008-11-04

    Provided are means for evaluating and identifying putative substrates of the twin arginine translocation (Tat) secretory pathway in Streptomyces and other bacterial species. Also provided, therefore, are simple ways to express, secrete and purify correctly folded heterologous proteins on a large scale using host microorganisms, such as, Streptomyces and the Tat pathway therein. Many of the thus-produced proteins are of significant therapeutic value in the pharmaceutical and biochemical industries, particularly when they can be secreted from the host in fully-folded active form. Accordingly, there are further provided the heterologous proteins produced by the Tat secretion pathway using the foregoing methods, and the computer algorithm used to identify the Tat signal sequence and putative substrates.

  5. Biosynthetic Pathways of Ergot Alkaloids

    PubMed Central

    Gerhards, Nina; Neubauer, Lisa; Tudzynski, Paul; Li, Shu-Ming

    2014-01-01

    Ergot alkaloids are nitrogen-containing natural products belonging to indole alkaloids. The best known producers are fungi of the phylum Ascomycota, e.g., Claviceps, Epichloë, Penicillium and Aspergillus species. According to their structures, ergot alkaloids can be divided into three groups: clavines, lysergic acid amides and peptides (ergopeptines). All of them share the first biosynthetic steps, which lead to the formation of the tetracyclic ergoline ring system (except the simplest, tricyclic compound: chanoclavine). Different modifications on the ergoline ring by specific enzymes result in an abundance of bioactive natural products, which are used as pharmaceutical drugs or precursors thereof. From the 1950s through to recent years, most of the biosynthetic pathways have been elucidated. Gene clusters from several ergot alkaloid producers have been identified by genome mining and the functions of many of those genes have been demonstrated by knock-out experiments or biochemical investigations of the overproduced enzymes. PMID:25513893

  6. Biosynthetic pathways of ergot alkaloids.

    PubMed

    Gerhards, Nina; Neubauer, Lisa; Tudzynski, Paul; Li, Shu-Ming

    2014-01-01

    Ergot alkaloids are nitrogen-containing natural products belonging to indole alkaloids. The best known producers are fungi of the phylum Ascomycota, e.g., Claviceps, Epichloë, Penicillium and Aspergillus species. According to their structures, ergot alkaloids can be divided into three groups: clavines, lysergic acid amides and peptides (ergopeptines). All of them share the first biosynthetic steps, which lead to the formation of the tetracyclic ergoline ring system (except the simplest, tricyclic compound: chanoclavine). Different modifications on the ergoline ring by specific enzymes result in an abundance of bioactive natural products, which are used as pharmaceutical drugs or precursors thereof. From the 1950s through to recent years, most of the biosynthetic pathways have been elucidated. Gene clusters from several ergot alkaloid producers have been identified by genome mining and the functions of many of those genes have been demonstrated by knock-out experiments or biochemical investigations of the overproduced enzymes. PMID:25513893

  7. An evidence-based knowledgebase of pulmonary arterial hypertension to identify genes and pathways relevant to pathogenesis† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c3mb70496c Click here for additional data file.

    PubMed Central

    Zhao, Min; Austin, Eric D.; Hemnes, Anna R.; Loyd, James E.

    2014-01-01

    Pulmonary arterial hypertension (PAH) is a major progressive form of pulmonary hypertension (PH) with more than 4800 patients in the United States. In the last two decades, many studies have identified numerous genes associated with this disease. However, there is no comprehensive research resource for PAH or other PH types that integrates various genetic studies and their related biological information. Thus, the number of associated genes, and their strength of evidence, is unclear. In this study, we tested the hypothesis that a web-based knowledgebase could be used to develop a biological map of highly interrelated, functionally important genes in PAH. We developed the pulmonary arterial hypertension knowledgebase (PAHKB, http://bioinfo.mc.vanderbilt.edu/PAHKB/), a comprehensive database with a user-friendly web interface. PAHKB extracts genetic data from all available sources, including those from association studies, genetic mutation, gene expression, animal model, supporting literature, various genomic annotations, gene networks, cellular and regulatory pathways, as well as microRNAs. Moreover, PAHKB provides online tools for data browsing and searching, data integration, pathway graphical presentation, and gene ranking. In the current release, PAHKB contains 341 human PH-related genes (293 protein coding and 48 non-coding genes) curated from over 1000 PubMed abstracts. Based on the top 39 ranked PAH-related genes in PAHKB, we constructed a core biological map. This core map was enriched with the TGF-beta signaling pathway, focal adhesion, cytokine–cytokine receptor interaction, and MAPK signaling. In addition, the reconstructed map elucidates several novel cancer signaling pathways, which may provide clues to support the application of anti-cancer therapeutics to PAH. In summary, we have developed a system for the identification of core PH-related genes and identified critical signaling pathways that may be relevant to PAH pathogenesis. This system can be easily applied to other pulmonary diseases. PMID:24448676

  8. Morphoproteomics identifies constitutive activation of the mTORC2/Akt and NF-?B pathways and expressions of IGF-1R, Sirt1, COX-2, and FASN in peripheral T-cell lymphomas: pathogenetic implications and therapeutic options

    PubMed Central

    Quesada, Andrés E; Nguyen, Nghia D; Rios, Adan; Brown, Robert E

    2014-01-01

    Background: Gaining a better understanding of the molecular circuitries and pathways implicated in the malignant growth and biological behavior of T cell lymphomas may identify potential cellular targets with clinical therapeutic potential. The immunohistochemical characterization of key cellular proteins participating in these pathways can provide surrogate markers of biological activity. The mammalian target of rapamycin complex (mTORC) signaling pathway has been implicated in T-cell lymphopoiesis. The mTORC2 pathway involves downstream activation of nuclear factor (NF)-?B and p-Akt (Ser 473). Fatty acid synthase (FASN) and insulin-like growth factor-1 receptor (IGF-1R) are expressed upstream of the mTORC and NF-?B signaling pathways. Cyclooxygenase (COX)-2 products influence these pathways. Our goal was to use morphoproteomics to characterize the expression patterns of the proteins in various peripheral T-cell lymphomas. Design: Ten cases of peripheral T-cell lymphoma (PTCL) were examined for expression of proteins along the mTORC, Akt and NF-?B pathways and affiliated tumorigenic molecules. These included two angioimmunoblastic PTCL, one natural killer/PTCL, one anaplastic large PTCL, and six PTCL not otherwise specified. Immunostaining for phosphorylated (p) mTOR (Ser 2448), p-Akt (Ser 473), p-NF-?Bp65 (Ser 536), IGF-1R (Tyr1165/1166), silent mating type information regulation 2 homolog 1 (Sirt1), COX-2 and FASN was performed on paraffin-embedded tissue for each case. Percent expression was scored using bright-field microscopy with high expression designated as more than 50% of the cells with positive stain in the appropriate subcellular compartment. Results: All ten cases demonstrated nuclear staining for p-mTOR (Ser 2448) corresponding to mTORC 2, and all cases showed strong, diffuse nuclear staining for p-NF-?Bp65 (Ser 536). All ten also showed nuclear and cytoplasmic staining for p-Akt (Ser 473) and cytoplasmic staining for IGF-1R. High expressions for nuclear Sirt1, and cytoplasmic COX-2 and FASN were detected in 7, 9, and 8 out of 10 cases, respectively. Six out of 10 cases demonstrated high expression of all the mentioned markers. Conclusion: The constitutive activation of mTORC2, NF-?B, p-Akt and the concomitant expression of IGF-1R suggests convergence of these molecular pathways in T-cell lymphoma. The results of this study also suggest that mTORC2 may be a common denominator among this heterogeneous group of lymphomas. Interference of key nodes of this pathway may carry a clinical therapeutic benefit. Agents that may be considered based on existing data include: bortezomib to inhibit NF-?B pathway activation; metformin to inhibit both NF-?B and mTORC2 and histone deacteylase inhibitors to inhibit mTORC2 pathway signaling. Furthermore, panobinostat inhibits Sirt1 pathway when present, and celecoxib inhibits NF-?B pathway activation independent of COX2. PMID:25674239

  9. Combinatorial genetic transformation generates a library of metabolic phenotypes for the carotenoid pathway in maize

    PubMed Central

    Zhu, Changfu; Naqvi, Shaista; Breitenbach, Jürgen; Sandmann, Gerhard; Christou, Paul; Capell, Teresa

    2008-01-01

    Combinatorial nuclear transformation is a novel method for the rapid production of multiplex-transgenic plants, which we have used to dissect and modify a complex metabolic pathway. To demonstrate the principle, we transferred 5 carotenogenic genes controlled by different endosperm-specific promoters into a white maize variety deficient for endosperm carotenoid synthesis. We recovered a diverse population of transgenic plants expressing different enzyme combinations and showing distinct metabolic phenotypes that allowed us to identify and complement rate-limiting steps in the pathway and to demonstrate competition between ?-carotene hydroxylase and bacterial ?-carotene ketolase for substrates in 4 sequential steps of the extended pathway. Importantly, this process allowed us to generate plants with extraordinary levels of ?-carotene and other carotenoids, including complex mixtures of hydroxycarotenoids and ketocarotenoids. Combinatorial transformation is a versatile approach that could be used to modify any metabolic pathway and pathways controlling other biochemical, physiological, or developmental processes. PMID:19011084

  10. Combined miRNA and mRNA Signature Identifies Key Molecular Players and Pathways Involved in Chikungunya Virus Infection in Human Cells

    PubMed Central

    Saxena, Tanvi; Tandon, Bhavna; Sharma, Shivani; Chameettachal, Shibu; Ray, Pratima; Ray, Alok R.; Kulshreshtha, Ritu

    2013-01-01

    Since its discovery, Chikungunya fever caused by a virus (CHIKV) has ravaged most of Africa and Southeast Asia. Despite there being more than a million reported cases in India alone and the seriousness of the disease in the chronic phase, a clear understanding of the disease pathogenesis and host response remains elusive. Here, we use microarray technology and quantitative PCR method to establish the complete miRNA, snoRNA and mRNA signature of host response upon CHIKV infection in human cell line infection model, HEK293T. The results were further validated in human primary cells (dermal fibroblasts). miRNA expression profiling revealed regulation of 152 miRNAs post CHIKV infection. An interesting overlap in miRNA signature was seen majorly with HCV, HPV and HIV1 virus. The microarray data further validated by qRT-PCR revealed induction of miR-744, miR-638, miR-503 and others among the top upregulated miRNAs. Notably, we found induction of snoRNAs belonging to C/D cluster including close paralogs of U3, U44, U76 and U78 snoRNAs. Genes were found to be differentially expressed along 3 major pathways; TGF-?, endocytosis and the cell cycle pathways. qRT-PCR data confirmed strong induction of TGF-? (SMAD6, JUN, SKIL) and endocytosis pathway (CXCR4, HSPA8, ADRB1) genes while downregulation of cell cycle genes (CDC27 and CDC23). Interestingly, use of TGF-? inhibitor, SB-431542, increased CHIKV mediated cell death. Overall, this study aims at providing the first complete transcriptome signature of host response upon CHIKV infection to aid identification of possible biomarkers and therapeutic targets. PMID:24278205

  11. The endocytic pathway mediates cell entry of dsRNA to induce RNAi silencing

    Microsoft Academic Search

    Maria-Carla Saleh; Ronald P. van Rij; Armin Hekele; Amethyst Gillis; Edan Foley; Patrick H. O'Farrell; Raul Andino

    2006-01-01

    Many metazoan cells can take up exogenous double-stranded (ds) RNA and use it to initiate an RNA silencing response, however, the mechanism for this uptake is ill-defined. Here, we identify the pathway for dsRNA uptake in Drosophila melanogaster S2 cells. Biochemical and cell biological analyses, and a genome-wide screen for components of the dsRNA-uptake machinery, indicated that dsRNA is taken

  12. Identifying beach sand sources and pathways in the San Francisco Bay Coastal System through the integration of bed characteristics, geochemical tracers, current measurements, and numerical modeling

    NASA Astrophysics Data System (ADS)

    Barnard, P.; Foxgrover, A. C.; Elias, E.; Erikson, L. H.; Hein, J. R.; McGann, M. L.; Mizell, K.; Rosenbauer, R. J.; Swarzenski, P. W.; Takesue, R. K.; Wong, F. L.; Woodrow, D. L.

    2012-12-01

    A unique, multi-faceted provenance study was performed to definitively establish the primary sources, sinks, and transport pathways of beach sized-sand in the San Francisco Bay Coastal System. This integrative program is based on comprehensive surficial sediment sampling of the San Francisco Bay Coastal System, including the seabed, bay floor, area beaches, adjacent rock units, and major drainages. Analyses of sample morphometrics and biological composition (e.g., foraminifera) were then integrated with a suite of tracers including 87Sr/86Sr and 143Nd/144Nd isotopes, rare earth elements, semi-quantitative X-ray diffraction mineralogy, and heavy minerals, and with process-based numerical modeling, in situ current measurements, and bedform asymmetry, to robustly determine the provenance of beach-sized sand in the region. Cross-validating geochemical analyses, numerical modeling, physical process measurements, and proxy-based techniques (e.g., bedform asymmetry, grain size morphometrics) is proved an effective technique for confidently defining sources, pathways, and sinks of sand in complex coastal-estuarine systems. The consensus results highlight the regional impact of a sharp reduction in the primary sediment source, the Sierras, to the San Francisco Bay Coastal System over the last century in driving erosion of the bay floor, ebb-tidal delta, and the outer coast south of the Golden Gate.A) Calculated transport directions based on the integration of the provenance techniques. B) Number of techniques applied for each grid cell to determine the final transport directions.

  13. Glycosidic intermediates identified in 1H MR spectra of intact tumour cells may contribute to the clarification of aspects of glycosylation pathways.

    PubMed

    Grande, Sveva; Palma, Alessandra; Luciani, Anna Maria; Rosi, Antonella; Guidoni, Laura; Viti, Vincenza

    2011-01-01

    The glycosylation process, through the addition of carbohydrates, is a major post-translational modification of proteins and glycolipids. Proteins may be glycosylated in either the secretory pathway leading to N-linked or O-linked glycoproteins or as nucleocytoplasmic glycosylation that targets only single proteins involving a single ?-linked N-acetylglucosamine. In both cases, the key precursors are the uridine diphospho-N-acetylhexosamines synthesised by the hexosamine biosynthetic pathway. Furthermore, uridine diphospho-N-acetylglucosamine participates in the biosynthesis of sialic acid. In this work, we propose MRS for the detection of uridine diphospho-N-acetylhexosamines visible in high-resolution MR spectra of intact cells from different human tumours. Signals from the nucleotide and amino sugar moieties, including amide signals observed for the first time in whole cells, are assigned, also taking advantage of spectral changes that follow cell treatment with ammonium chloride. Finally, parallel changes in uridine diphospho-N-acetylhexosamines and glutamine pools, observed after pH changes induced by ammonium chloride in the different tumour cell lines, may provide more details on the glycosylation processes. PMID:20669171

  14. Adverse Outcome Pathways: From Definition to Application

    EPA Science Inventory

    A challenge for both human health and ecological toxicologists is the transparent application of mechanistic (e.g., molecular, biochemical, histological) data to risk assessments. The adverse outcome pathway (AOP) is a conceptual framework designed to meet this need. Specifical...

  15. 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.

  16. Biochemical transformation of coals

    DOEpatents

    Lin, Mow S. (Rocky Point, NY); Premuzic, Eugene T. (East Moriches, NY)

    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.

  17. Compound library screening identified Akt/PKB kinase pathway inhibitors as potential key molecules for the development of new chemotherapeutics against schistosomiasis

    PubMed Central

    Morel, Marion; Vanderstraete, Mathieu; Cailliau, Katia; Lescuyer, Arlette; Lancelot, Julien; Dissous, Colette

    2014-01-01

    Protein kinases (PKs) are one of the largest protein families in most eukaryotic organisms. These enzymes are involved in the control of cell proliferation, differentiation and metabolism and a large number of the anticancer drugs currently used are directed against PKs. The structure and function of PKs are well conserved throughout evolution. In schistosome parasites, PKs were shown to be involved in essential functions at every stage of the parasite life cycle, making these enzymes promising anti-parasite drug targets. In this study, we tested a panel of commercial inhibitors for various PKs and analyzed their effects on pairing and egg production by schistosomes as well as their toxicity towards schistosomula larvae. Results obtained confirmed the deleterious effect of PK targeting on Schistosoma mansoni physiology and the important function of different tyrosine and serine/threonine kinases in the biology and reproduction of this parasite. They also indicated for the first time that the Protein kinase B (also called Akt) which is a major downstream target of many receptor tyrosine kinases and a central player at the crossroads of signal transduction pathways activated in response to growth factors and insulin, can constitute a novel target for anti-schistosome chemotherapy. Structural and functional studies have shown that SmAkt is a conserved kinase and that its activity can be inhibited by commercially available Akt inhibitors. In treated adult worms, Akt/PKB kinase pathway inhibitors induced profound alterations in pairing and egg laying and they also greatly affected the viability of schistosomula larvae. PMID:25516836

  18. Molecular and biochemical characterization of tomato farnesyl-protein transferase.

    PubMed Central

    Schmitt, D; Callan, K; Gruissem, W

    1996-01-01

    The prenylation of membrane-associated proteins involved in the regulation of eukaryotic cell growth and signal transduction is critically important for their subcellular localization and biological activity. In contrast to mammalian cells and yeast, however, the function of protein prenylation in plants is not well understood and only a few prenylated proteins have been identified. We partially purified and characterized farnesyl-protein transferase from tomato (Lycopersicon esculentum, LeFTase) to analyze its biochemical and molecular properties. Using Ras- and G gamma-specific peptide substrates and competition assays we showed that tomato protein extracts have both farnesyl-protein transferase and geranylgeranyl-protein transferase 1 activities. Compared with the heterologous synthetic peptide substrates, the plant-specific CaaX sequence of the ANJ1 protein is a less efficient substrate for LeFTase in vitro. LeFTase activity profiles and LeFTase beta-subunit protein (LeFTB) levels differ significantly in various tissues and are regulated during fruit development. Partially purified LeFTase requires Zn2+ and Mg2+ for enzymatic activity and has an apparent molecular mass of 100 kD Immunoprecipitation experiments using anti-alpha LeFTB antibodies confirmed that LeFTB is a component of LeFTase but not of tomato geranylgeranyl-protein transferase 1. Based on their conserved bio-chemical activities, we expect that prenyltransferases are likely integrated with the sterol biosynthesis pathway in the control of plant cell growth. PMID:8883388

  19. A biochemical framework for RNA silencing in plants

    Microsoft Academic Search

    Guiliang Tang; Brenda J. Reinhart; David P. Bartel; Phillip D. Zamore

    2003-01-01

    RNA silencing phenomena were first discovered in plants, yet only the RNA interference pathway in animals has been subject to biochemical analysis. Here, we extend biochemical analysis to plant RNA silencing. We find that standard wheat germ extract contains Dicer-like enzymes that convert double-stranded RNA (dsRNA) into two classes of small interfering RNAs, as well as an RNA-dependent RNA polymerase

  20. Putative cold acclimation pathways in Arabidopsis thaliana identified by a combined analysis of mRNA co-expression patterns, promoter motifs and transcription factors

    Microsoft Academic Search

    Aakash Chawade; Marcus Bräutigam; Angelica Lindlöf; Olof Olsson; Björn Olsson

    2007-01-01

    BACKGROUND: With the advent of microarray technology, it has become feasible to identify virtually all genes in an organism that are induced by developmental or environmental changes. However, relying solely on gene expression data may be of limited value if the aim is to infer the underlying genetic networks. Development of computational methods to combine microarray data with other information

  1. Phenotype-driven chemical screening in zebrafish for compounds that inhibit collective cell migration identifies multiple pathways potentially involved in metastatic invasion

    PubMed Central

    Gallardo, Viviana E.; Varshney, Gaurav K.; Lee, Minnkyong; Bupp, Sujata; Xu, Lisha; Shinn, Paul; Crawford, Nigel P.; Inglese, James; Burgess, Shawn M.

    2015-01-01

    ABSTRACT In the last decade, high-throughput chemical screening has become the dominant approach for discovering novel compounds with therapeutic properties. Automated screening using in vitro or cultured cell assays have yielded thousands of candidate drugs for a variety of biological targets, but these approaches have not resulted in an increase in drug discovery despite major increases in expenditures. In contrast, phenotype-driven screens have shown a much stronger success rate, which is why we developed an in vivo assay using transgenic zebrafish with a GFP-marked migrating posterior lateral line primordium (PLLp) to identify compounds that influence collective cell migration. We then conducted a high-throughput screen using a compound library of 2160 annotated bioactive synthetic compounds and 800 natural products to identify molecules that block normal PLLp migration. We identified 165 compounds that interfere with primordium migration without overt toxicity in vivo. Selected compounds were confirmed in their migration-blocking activity by using additional assays for cell migration. We then proved the screen to be successful in identifying anti-metastatic compounds active in vivo by performing orthotopic tumor implantation assays in mice. We demonstrated that the Src inhibitor SU6656, identified in our screen, can be used to suppress the metastatic capacity of a highly aggressive mammary tumor cell line. Finally, we used CRISPR/Cas9-targeted mutagenesis in zebrafish to genetically validate predicted targets of compounds. This approach demonstrates that the migrating PLLp in zebrafish can be used for large-scale, high-throughput screening for compounds that inhibit collective cell migration and, potentially, anti-metastatic compounds. PMID:25810455

  2. Phenotype-driven chemical screening in zebrafish for compounds that inhibit collective cell migration identifies multiple pathways potentially involved in metastatic invasion.

    PubMed

    Gallardo, Viviana E; Varshney, Gaurav K; Lee, Minnkyong; Bupp, Sujata; Xu, Lisha; Shinn, Paul; Crawford, Nigel P; Inglese, James; Burgess, Shawn M

    2015-06-01

    In the last decade, high-throughput chemical screening has become the dominant approach for discovering novel compounds with therapeutic properties. Automated screening using in vitro or cultured cell assays have yielded thousands of candidate drugs for a variety of biological targets, but these approaches have not resulted in an increase in drug discovery despite major increases in expenditures. In contrast, phenotype-driven screens have shown a much stronger success rate, which is why we developed an in vivo assay using transgenic zebrafish with a GFP-marked migrating posterior lateral line primordium (PLLp) to identify compounds that influence collective cell migration. We then conducted a high-throughput screen using a compound library of 2160 annotated bioactive synthetic compounds and 800 natural products to identify molecules that block normal PLLp migration. We identified 165 compounds that interfere with primordium migration without overt toxicity in vivo. Selected compounds were confirmed in their migration-blocking activity by using additional assays for cell migration. We then proved the screen to be successful in identifying anti-metastatic compounds active in vivo by performing orthotopic tumor implantation assays in mice. We demonstrated that the Src inhibitor SU6656, identified in our screen, can be used to suppress the metastatic capacity of a highly aggressive mammary tumor cell line. Finally, we used CRISPR/Cas9-targeted mutagenesis in zebrafish to genetically validate predicted targets of compounds. This approach demonstrates that the migrating PLLp in zebrafish can be used for large-scale, high-throughput screening for compounds that inhibit collective cell migration and, potentially, anti-metastatic compounds. PMID:25810455

  3. Genetic analysis of photoreceptor action pathways in Arabidopsis thaliana

    SciTech Connect

    Not Available

    1991-01-01

    The specific strategies and long-term goals of this proposal remain intact relative to the original proposal. We continue to isolate and characterize photomorphogenic mutants of Arabidopsis thaliana. The molecular and biochemical characterization of one of these mutants, det1, has led to one publication of original data and to one Society for Experimental Biology Symposium paper (see below). The phenotype of a second mutant, det2, has also been studied during this funding period. In addition, we have continued work on a general strategy to isolate mutations in trans-acting regulatory factors that mediate light-regulated gene expression, and have identified several potentially interesting regulatory mutants. In the third funding period, we will concentrate on the genetical, biochemical, and molecular characterization of these new mutants. Construction of double mutants between the new mutants and the previously characterized morphological mutants should allow us to construct a pathway for light-regulated seedling development in Arabidopsis.

  4. Mutations in Escherichia coli ExbB transmembrane domains identify scaffolding and signal transduction functions and exclude participation in a proton pathway.

    PubMed

    Baker, Kristin R; Postle, Kathleen

    2013-06-01

    The TonB system couples cytoplasmic membrane proton motive force (pmf) to active transport of diverse nutrients across the outer membrane. Current data suggest that cytoplasmic membrane proteins ExbB and ExbD harness pmf energy. Transmembrane domain (TMD) interactions between TonB and ExbD allow the ExbD C terminus to modulate conformational rearrangements of the periplasmic TonB C terminus in vivo. These conformational changes somehow allow energization of high-affinity TonB-gated transporters by direct interaction with TonB. While ExbB is essential for energy transduction, its role is not well understood. ExbB has N-terminus-out, C-terminus-in topology with three TMDs. TMDs 1 and 2 are punctuated by a cytoplasmic loop, with the C-terminal tail also occupying the cytoplasm. We tested the hypothesis that ExbB TMD residues play roles in proton translocation. Reassessment of TMD boundaries based on hydrophobic character and residue conservation among distantly related ExbB proteins brought earlier widely divergent predictions into congruence. All TMD residues with potentially function-specific side chains (Lys, Cys, Ser, Thr, Tyr, Glu, and Asn) and residues with probable structure-specific side chains (Trp, Gly, and Pro) were substituted with Ala and evaluated in multiple assays. While all three TMDs were essential, they had different roles: TMD1 was a region through which ExbB interacted with the TonB TMD. TMD2 and TMD3, the most conserved among the ExbB/TolQ/MotA/PomA family, played roles in signal transduction between cytoplasm and periplasm and the transition from ExbB homodimers to homotetramers. Consideration of combined data excludes ExbB TMD residues from direct participation in a proton pathway. PMID:23603742

  5. Cross-talk between Wnt/?-catenin and Hippo signaling pathways: a brief review

    PubMed Central

    Kim, Minseong; Jho, Eek-hoon

    2014-01-01

    Department of Life Science, The University of Seoul, Seoul 130-743, Korea Balanced cell growth is crucial in animal development as well as tissue homeostasis. Concerted cross-regulation of multiple signaling pathways is essential for those purposes, and the dysregulation of signaling may lead to a variety of human diseases such as cancer. The time-honored Wnt/?-catenin and recently identified Hippo signaling pathways are evolutionarily conserved in both Drosophila and mammals, and are generally considered as having positive and negative roles in cell proliferation, respectively. While most mainstream regulators of the Wnt/?-catenin signaling pathway have been fairly well identified, the regulators of the Hippo pathway need to be more defined. The Hippo pathway controls organ size primarily by regulating cell contact inhibition. Recently, several crossregulations occurring between the Wnt/?-catenin and Hippo signaling pathways were determined through biochemical and genetic approaches. In the present mini-review, we mainly discuss the signal transduction mechanism of the Hippo signaling pathway, along with cross-talk between the regulators of the Wnt/?-catenin and Hippo signaling pathways. [BMB Reports 2014; 47(10): 540-545] PMID:25154721

  6. Identifying Calcium Channels and Porters in Plant Membranes

    SciTech Connect

    Sze, Heven

    1998-04-01

    The overall objectives of the proposal submitted in 6/90 was to understand how Ca was transported across plant membranes, and how these transport pathways were regulated. Ca participates in many cellular processes, including the transduction of hormonal and environmental signals, secretion, and protein folding. These processes depend on the coordination of passive Ca fluxes via channels and active Ca pumps; however these transport pathways are poorly understood in plants. We had, therefore, proposed to identify and characterize Ca transport proteins, such as the inositol-1 ,4,5-trisphosphate (IP3)-sensitive Ca channels and Ca pumps. We have had difficulties characterizing and cloning the IP3-sensitive Ca channel, but have made considerable progress on the biochemical characterization, and partial purification of a 120 kD Ca-pumping ATPase. We have begun to determine the structure of Ca pumps by molecular cloning and have already obtained a partial cDNA with features characteristic of Ca pumps.

  7. Biochemical analyses of indole-3-acetaldoxime-dependent auxin biosynthesis in Arabidopsis

    PubMed Central

    Sugawara, Satoko; Hishiyama, Shojiro; Jikumaru, Yusuke; Hanada, Atsushi; Nishimura, Takeshi; Koshiba, Tomokazu; Zhao, Yunde; Kamiya, Yuji; Kasahara, Hiroyuki

    2009-01-01

    Auxins are hormones that regulate many aspects of plant growth and development. The main plant auxin is indole-3-acetic acid (IAA), whose biosynthetic pathway is not fully understood. Indole-3-acetaldoxime (IAOx) has been proposed to be a key intermediate in the synthesis of IAA and several other indolic compounds. Genetic studies of IAA biosynthesis in Arabidopsis have suggested that 2 distinct pathways involving the CYP79B or YUCCA (YUC) genes may contribute to IAOx synthesis and that several pathways are also involved in the conversion of IAOx to IAA. Here we report the biochemical dissection of IAOx biosynthesis and metabolism in plants by analyzing IAA biosynthesis intermediates. We demonstrated that the majority of IAOx is produced by CYP79B genes in Arabidopsis because IAOx production was abolished in CYP79B-deficient mutants. IAOx was not detected from rice, maize, and tobacco, which do not have apparent CYP79B orthologues. IAOx levels were not significantly altered in the yuc1 yuc2 yuc4 yuc6 quadruple mutants, suggesting that the YUC gene family probably does not contribute to IAOx synthesis. We determined the pathway for conversion of IAOx to IAA by identifying 2 likely intermediates, indole-3-acetamide (IAM) and indole-3-acetonitrile (IAN), in Arabidopsis. When 13C6-labeled IAOx was fed to CYP79B-deficient mutants, 13C6 atoms were efficiently incorporated to IAM, IAN, and IAA. This biochemical evidence indicates that IAOx-dependent IAA biosynthesis, which involves IAM and IAN as intermediates, is not a common but a species-specific pathway in plants; thus IAA biosynthesis may differ among plant species. PMID:19279202

  8. Biochemical Applications in the Analytical Chemistry Lab

    ERIC Educational Resources Information Center

    Strong, Cynthia; Ruttencutter, Jeffrey

    2004-01-01

    An HPLC and a UV-visible spectrophotometer are identified as instruments that helps to incorporate more biologically-relevant experiments into the course, in order to increase the students understanding of selected biochemistry topics and enhances their ability to apply an analytical approach to biochemical problems. The experiment teaches…

  9. Pathways database system.

    PubMed

    Ozsoyoglu, Z Meral; Nadeau, Joseph H; Ozsoyoglu, G

    2003-01-01

    During the next phase of the Human Genome Project, research will focus on functional studies of attributing functions to genes, their regulatory elements, and other DNA sequences. To facilitate the use of genomic information in such studies, a new modeling perspective is needed to examine and study genome sequences in the context of many kinds of biological information. Pathways are the logical format for modeling and presenting such information in a manner that is familiar to biological researchers. In this paper, we introduce an integrated system, called "Pathways Database System," with a set of software tools for modeling, storing, analyzing, visualizing, and querying biological pathways data at different levels of genetic, molecular, biochemical and organismal detail. PMID:12831573

  10. Methods to identify molecular expression of mTOR pathway: a rationale approach to stratify patients affected by clear cell renal cell carcinoma for more likely response to mTOR inhibitors

    PubMed Central

    Fiorini, Claudia; Massari, Francesco; Pedron, Serena; Sanavio, Sara; Ciccarese, Chiara; Porcaro, Antonio Benito; Artibani, Walter; Bertoldo, Francesco; Zampini, Claudia; Sava, Teodoro; Ficial, Miriam; Caliò, Anna; Chilosi, Marco; D’Amuri, Alessandro; Sanguedolce, Francesca; Tortora, Giampaolo; Scarpa, Aldo; Delahunt, Brett; Porta, Camillo; Martignoni, Guido; Brunelli, Matteo

    2014-01-01

    Since target therapy with mTOR inhibitors plays an important role in the current management of clear cell renal cell carcinoma (RCC), there is an increasing demand for predictive biomarkers, which may help to select patients that are most likely to benefit from personalized treatment. When dealing with formalin-fixed paraffin-embedded (FFPE) cancer tissue specimens, several techniques may be used to identify potential molecular markers, yielding different outcome in terms of accuracy. We sought to investigate and compare the capability of three main techniques to detect molecules performing an active function in mTOR pathway in RCC. Immunohistochemistry (IHC), Western blot (WB) and immunofluorescence (IF) analyses were performed on FFPE RCC tissue specimens from 16 patients by using the following mTOR pathway-related: mTOR (Ser235/236), phospho-mTOR (p-mTOR/Ser2448), phospho-p70S6k (p-p70S6k/Thr389), both monoclonal and polyclonal, phospho-S6Rb (p-S6Rb) and phospho-4EBP1 (p-4EBP1/Thr37/46). No single molecule was simultaneously revealed by all three techniques. Only p-p70S6k was detected by two methods (IHC and IF) using a monoclonal antibody. The other molecules were detected exclusively by one technique, as follows: p-mTOR and polyclonal p-p70S6K by IHC, p70S6K, p-S6Rb and p-4EBP1 by WB, and, finally, mTOR by IF. We found significant differences in detecting mTOR pathway-related active biomarkers by using three common techniques such as IHC, WB and IF on RCC samples. Such results have important implications in terms of predictive biomarker testing, and need to be related to clinical end-points such as responsiveness to targeted drugs by prospective studies. PMID:25520878

  11. Validation of metabolic pathway databases based on chemical substructure search.

    PubMed

    Félix, Liliana; Valiente, Gabriel

    2007-09-01

    Metabolic pathway databases such as KEGG contain information on thousands of biochemical reactions drawn from the biomedical literature. Ensuring consistency of such large metabolic pathways is essential to their proper use. In this paper, we present a new method to determine consistency of an important class of biochemical reactions. Our method exploits the knowledge of the atomic rearrangement pattern in biochemical reactions, to reduce the automatic atom mapping problem to a series of chemical substructure searches between the substrate and the product of a biochemical reaction. As an illustrative application, we describe the exhaustive validation of a substantial portion from the latest release of the KEGG LIGAND database. PMID:17433774

  12. Transcriptional Responses of In Vivo Praziquantel Exposure in Schistosomes Identifies a Functional Role for Calcium Signalling Pathway Member CamKII

    PubMed Central

    You, Hong; McManus, Donald P.; Hu, Wei; Smout, Michael J.; Brindley, Paul J.; Gobert, Geoffrey N.

    2013-01-01

    Treatment for clinical schistosomiasis has relied centrally on the broad spectrum anthelmintic praziquantel; however, there is limited information on its mode of action or the molecular response of the parasite. This paper presents a transcriptional and functional approach to defining the molecular responses of schistosomes to praziquantel. Differential gene expression in Schistosoma japonicum was investigated by transcriptome-wide microarray analysis of adult worms perfused from infected mice after 0.5 to 24 hours after oral administration of sub-lethal doses of praziquantel. Genes up-regulated initially in male parasites were associated with “Tegument/Muscle Repair” and “Lipid/Ion Regulation” functions and were followed by “Drug Resistance” and “Ion Regulation” associated genes. Prominent responses induced in female worms included up-regulation of “Ca2+ Regulation” and “Drug Resistance” genes and later by transcripts of “Detoxification” and “Pathogen Defense” mechanisms. A subset of highly over-expressed genes, with putative drug resistance/detoxification roles or Ca2+-dependant/modulatory functions, were validated by qPCR. The leading candidate among these was CamKII, a putative calcium/calmodulin-dependent protein kinase type II delta chain. RNA interference was employed to knockdown CamKII in S. japonicum to determine the role of CamKII in the response to praziquantel. After partial-knockdown, schistosomes were analysed using IC50 concentrations (50% worm motility) and quantitative monitoring of parasite movement. When CamKII transcription was reduced by 50–69% in S. japonicum, the subsequent effect of an IC50 dosage of praziquantel was exacerbated, reducing motility from 47% to 27% in female worms and from 61% to 23% in males. These observations indicated that CamKII mitigates the effects of praziquantel, probably through stabilising Ca2+ fluxes within parasite muscles and tegument. Together, these studies comprehensively charted transcriptional changes upon exposure to praziquantel and, notably, identified CamKII as potentially central to the, as yet undefined, mode of action of praziquantel. PMID:23555262

  13. Switchgrass (Panicum virgatum) possesses a divergent family of cinnamoyl CoA reductases with distinct biochemical properties.

    PubMed

    Escamilla-Treviño, Luis L; Shen, Hui; Uppalapati, Srinivasa Rao; Ray, Tui; Tang, Yuhong; Hernandez, Timothy; Yin, Yanbin; Xu, Ying; Dixon, Richard A

    2010-01-01

    The down-regulation of enzymes of the monolignol pathway results in reduced recalcitrance of biomass for lignocellulosic ethanol production. Cinnamoyl CoA reductase (CCR) catalyzes the first step of the phenylpropanoid pathway specifically dedicated to monolignol biosynthesis. However, plants contain multiple CCR-like genes, complicating the selection of lignin-specific targets. This study was undertaken to understand the complexity of the CCR gene family in tetraploid switchgrass (Panicum virgatum) and to determine the biochemical properties of the encoded proteins. Four switchgrass cDNAs (most with multiple variants) encoding putative CCRs were identified by phylogenetic analysis, heterologously expressed in Escherichia coli, and the corresponding enzymes were characterized biochemically. Two cDNAs, PvCCR1 and PvCCR2, encoded enzymes with CCR activity. They are phylogenetically distinct, differentially expressed, and the corresponding enzymes exhibited different biochemical properties with regard to substrate preference. PvCCR1 has higher specific activity and prefers feruloyl CoA as substrate, whereas PvCCR2 prefers caffeoyl and 4-coumaroyl CoAs. Allelic variants of each cDNA were detected, but the two most diverse variants of PvCCR1 encoded enzymes with similar catalytic activity. Based on its properties and expression pattern, PvCCR1 is probably associated with lignin biosynthesis during plant development (and is therefore a target for the engineering of improved biomass), whereas PvCCR2 may function in defense. PMID:19761442

  14. Application of biochemical interactions in fossil fuels

    SciTech Connect

    Lin, M.S.; Premuzic, E.T.

    1994-12-31

    Certain extreme environments tolerant microorganisms interact with heavy crude oils by means of multiple biochemical reactions, asphaltenes, and bituminous materials. These reactions proceed via pathways which involve characteristic components of oils and coals such as asphaltenes, and in the chemically related constituents found in bituminous coals. These chemical components serve as markers of the interactions between microorganisms and fossil fuels. Studies in which temperature, pressure, and salinity tolerant microorganisms have been allowed to interact with different crude oils and bituminous coals, have shown that biochemically induced changes occur in the distribution of hydrocarbons and in the chemical nature of organometallic and heterocyclic compounds. Such structural chemical rearrangements have direct applications in monitoring the efficiency, the extent, and the chemical nature of the fossil fuels bioconversion. Recent developments of chemical marker applications in the monitoring of fossil fuels bioconversion will be discussed.

  15. Nonlinear Biochemical Signal Processing via Noise Propagation

    E-print Network

    Kyung Hyuk Kim; Hong Qian; Herbert M. Sauro

    2013-09-10

    Single-cell studies often show significant phenotypic variability due to the stochastic nature of intra-cellular biochemical reactions. When the numbers of molecules, e.g., transcription factors and regulatory enzymes, are in low abundance, fluctuations in biochemical activities become significant and such "noise" can propagate through regulatory cascades in terms of biochemical reaction networks. Here we develop an intuitive, yet fully quantitative method for analyzing how noise affects cellular phenotypes based on identifying a system's nonlinearities and noise propagations. We observe that such noise can simultaneously enhance sensitivities in one behavioral region while reducing sensitivities in another. Employing this novel phenomenon we designed three biochemical signal processing modules: (a) A gene regulatory network that acts as a concentration detector with both enhanced amplitude and sensitivity. (b) A non-cooperative positive feedback system, with a graded dose-response in the deterministic case, that serves as a bistable switch due to noise-induced bimodality. (c) A noise-induced linear amplifier for gene regulation that requires no feedback. The methods developed in the present work allow one to understand and engineer nonlinear biochemical signal processors based on fluctuation-induced phenotypes.

  16. Biochemical and Structural Characterization of the Arabidopsis Bifunctional Enzyme Dethiobiotin

    E-print Network

    Paris-Sud XI, Université de

    Biochemical and Structural Characterization of the Arabidopsis Bifunctional Enzyme Dethiobiotin by a single enzyme encoded by a bifunctional gene originating from the fusion of prokaryotic monofunctional of a bifunctional enzyme in biotin synthesis pathway in eukaryotes and the relative implication of each

  17. Potential drug targets in Mycobacterium tuberculosis through metabolic pathway analysis

    Microsoft Academic Search

    Sharmila Anishetty; Mrudula Pulimi; Pennathur Gautam

    2005-01-01

    The emergence of multidrug resistant varieties of Mycobacterium tuberculosis has led to a search for novel drug targets. We have performed an insilico comparative analysis of metabolic pathways of the host Homo sapiens and the pathogen M. tuberculosis. Enzymes from the biochemical pathways of M. tuberculosis from the KEGG metabolic pathway database were compared with proteins from the hostH. sapiens,

  18. Biochemical upgrading of oils

    DOEpatents

    Premuzic, E.T.; Lin, M.S.

    1999-01-12

    A process for biochemical conversion of heavy crude oils is provided. The process includes contacting heavy crude oils with adapted biocatalysts. The resulting upgraded oil shows, a relative increase in saturated hydrocarbons, emulsions and oxygenates and a decrease in compounds containing organic sulfur, organic nitrogen and trace metals. Adapted microorganisms which have been modified under challenged growth processes are also disclosed. 121 figs.

  19. Nanoparticles as biochemical sensors

    PubMed Central

    El-Ansary, Afaf; Faddah, Layla M

    2010-01-01

    There is little doubt that nanoparticles offer real and new opportunities in many fields, such as biomedicine and materials science. Such particles are small enough to enter almost all areas of the body, including cells and organelles, potentially leading to new approaches in nanomedicine. Sensors for small molecules of biochemical interest are of critical importance. This review is an attempt to trace the use of nanomaterials in biochemical sensor design. The possibility of using nanoparticles functionalized with antibodies as markers for proteins will be elucidated. Moreover, capabilities and applications for nanoparticles based on gold, silver, magnetic, and semiconductor materials (quantum dots), used in optical (absorbance, luminescence, surface enhanced Raman spectroscopy, surface plasmon resonance), electrochemical, and mass-sensitive sensors will be highlighted. The unique ability of nanosensors to improve the analysis of biochemical fluids is discussed either through considering the use of nanoparticles for in vitro molecular diagnosis, or in the biological/biochemical analysis for in vivo interaction with the human body. PMID:24198472

  20. Biochemical upgrading of oils

    DOEpatents

    Premuzic, Eugene T. (East Moriches, NY); Lin, Mow S. (Rocky Point, NY)

    1999-01-12

    A process for biochemical conversion of heavy crude oils is provided. The process includes contacting heavy crude oils with adapted biocatalysts. The resulting upgraded oil shows, a relative increase in saturated hydrocarbons, emulsions and oxygenates and a decrease in compounds containing in organic sulfur, organic nitrogen and trace metals. Adapted microorganisms which have been modified under challenged growth processes are also disclosed.

  1. Elucidation of an Alternate Isoleucine Biosynthesis Pathway in Geobacter sulfurreducens?

    PubMed Central

    Risso, Carla; Van Dien, Stephen J.; Orloff, Amber; Lovley, Derek R.; Coppi, Maddalena V.

    2008-01-01

    The central metabolic model for Geobacter sulfurreducens included a single pathway for the biosynthesis of isoleucine that was analogous to that of Escherichia coli, in which the isoleucine precursor 2-oxobutanoate is generated from threonine. 13C labeling studies performed in G. sulfurreducens indicated that this pathway accounted for a minor fraction of isoleucine biosynthesis and that the majority of isoleucine was instead derived from acetyl-coenzyme A and pyruvate, possibly via the citramalate pathway. Genes encoding citramalate synthase (GSU1798), which catalyzes the first dedicated step in the citramalate pathway, and threonine ammonia-lyase (GSU0486), which catalyzes the conversion of threonine to 2-oxobutanoate, were identified and knocked out. Mutants lacking both of these enzymes were auxotrophs for isoleucine, whereas single mutants were capable of growth in the absence of isoleucine. Biochemical characterization of the single mutants revealed deficiencies in citramalate synthase and threonine ammonia-lyase activity. Thus, in G. sulfurreducens, 2-oxobutanoate can be synthesized either from citramalate or threonine, with the former being the main pathway for isoleucine biosynthesis. The citramalate synthase of G. sulfurreducens constitutes the first characterized member of a phylogenetically distinct clade of citramalate synthases, which contains representatives from a wide variety of microorganisms. PMID:18245290

  2. Mercury methylation independent of the acetyl-coenzyme A pathway in sulfate-reducing bacteria.

    PubMed

    Ekstrom, Eileen B; Morel, François M M; Benoit, Janina M

    2003-09-01

    Sulfate-reducing bacteria (SRB) in anoxic waters and sediments are the major producers of methylmercury in aquatic systems. Although a considerable amount of work has addressed the environmental factors that control methylmercury formation and the conditions that control bioavailability of inorganic mercury to SRB, little work has been undertaken analyzing the biochemical mechanism of methylmercury production. The acetyl-coenzyme A (CoA) pathway has been implicated as being key to mercury methylation in one SRB strain, Desulfovibrio desulfuricans LS, but this result has not been extended to other SRB species. To probe whether the acetyl-CoA pathway is the controlling biochemical process for methylmercury production in SRB, five incomplete-oxidizing SRB strains and two Desulfobacter strains that do not use the acetyl-CoA pathway for major carbon metabolism were assayed for methylmercury formation and acetyl-CoA pathway enzyme activities. Three of the SRB strains were also incubated with chloroform to inhibit the acetyl-CoA pathway. So far, all species that have been found to have acetyl-CoA activity are complete oxidizers that require the acetyl-CoA pathway for basic metabolism, as well as methylate mercury. Chloroform inhibits Hg methylation in these species either by blocking the methylating enzyme or by indirect effects on metabolism and growth. However, we have identified four incomplete-oxidizing strains that clearly do not utilize the acetyl-CoA pathway either for metabolism or mercury methylation (as confirmed by the absence of chloroform inhibition). Hg methylation is thus independent of the acetyl-CoA pathway and may not require vitamin B(12) in some and perhaps many incomplete-oxidizing SRB strains. PMID:12957930

  3. Induction of ?Np63 by the Newly Identified Keratinocyte-Specific Transforming Growth Factor ? Signaling Pathway with Smad2 and I?B Kinase ? in Squamous Cell Carcinoma12

    PubMed Central

    Fukunishi, Nahoko; Katoh, Iyoko; Tomimori, Yoshiya; Tsukinoki, Keiichi; Hata, Ryu-Ichiro; Nakao, Atsuhito; Ikawa, Yoji; Kurata, Shun-ichi

    2010-01-01

    The expression of p63 (TP63/p51) occurs in the basal cells of stratified epithelia and is strongly enhanced at the early stages of squamous cell carcinomas (SCCs) of the head and neck, skin, cervix, and others. We analyzed a promoter/enhancer region (2k?N) that drives the predominant expression of ?Np63 for sensitivity to Smad signaling pathways. Reporter assays in HepG2 cells showed a moderate activation of 2k?N by Smad2 and I?B kinase ? (IKK?), partners of the newly identified keratinocyte-specific transforming growth factor ? (TGF-?) signaling, but not by other Smad molecules. In A431 cells, 2k?N was activated by Smad2 and IKK?, for which a Smad binding element (SMD2) at -204 was essential. Binding of Smad2 to the chromosomal SMD2 site was detectable. The association of Smad2 with IKK? was evident in the nucleus of A431, accounting for the enhancement of ?Np63 expression by TGF-?. Moreover, both ?Np63 and IKK? were necessary to maintain the noninvasive phenotype of this cell line. FaDu, an invasive, Smad4-deficient SCC, also allowed 2k?N transactivation by transfected Smad2 in the presence of endogenous IKK?. Reflecting the lack of chromosomal SMD2-Smad2 association and the absence of nuclear IKK?, however, endogenous ?Np63 was not controlled by TGF-? or IKK? in FaDu. SCC tissue arrays showed nuclear accumulation of IKK? and p63 intensification in well-differentiated noninvasive lesions. This study indicates that p63 is a target gene of the proposed keratinocyte-specific TGF-? signal pathway for suppression of the malignant conversion of SCC. PMID:21170261

  4. Biochemical characterization of the maltokinase from Mycobacterium bovis BCG

    PubMed Central

    2010-01-01

    Background Maltose-1-phosphate was detected in Mycobacterium bovis BCG extracts in the 1960's but a maltose-1-phosphate synthetase (maltokinase, Mak) was only much later purified from Actinoplanes missouriensis, allowing the identification of the mak gene. Recently, this metabolite was proposed to be the intermediate in a pathway linking trehalose with the synthesis of glycogen in M. smegmatis. Although the M. tuberculosis H37Rv mak gene (Rv0127) was considered essential for growth, no mycobacterial Mak has, to date, been characterized. Results The sequence of the Mak from M. bovis BCG was identical to that from M. tuberculosis strains (99-100% amino acid identity). The enzyme was dependent on maltose and ATP, although GTP and UTP could be used to produce maltose-1-phosphate, which we identified by TLC and characterized by NMR. The Km for maltose was 2.52 ± 0.40 mM and 0.74 ± 0.12 mM for ATP; the Vmax was 21.05 ± 0.89 ?mol/min.mg-1. Divalent cations were required for activity and Mg2+ was the best activator. The enzyme was a monomer in solution, had maximal activity at 60°C, between pH 7 and 9 (at 37°C) and was unstable on ice and upon freeze/thawing. The addition of 50 mM NaCl markedly enhanced Mak stability. Conclusions The unknown role of maltokinases in mycobacterial metabolism and the lack of biochemical data led us to express the mak gene from M. bovis BCG for biochemical characterization. This is the first mycobacterial Mak to be characterized and its properties represent essential knowledge towards deeper understanding of mycobacterial physiology. Since Mak may be a potential drug target in M. tuberculosis, its high-level production and purification in bioactive form provide important tools for further functional and structural studies. PMID:20507595

  5. Electronic modulation of biochemical signal generation

    NASA Astrophysics Data System (ADS)

    Gordonov, Tanya; Kim, Eunkyoung; Cheng, Yi; Ben-Yoav, Hadar; Ghodssi, Reza; Rubloff, Gary; Yin, Jun-Jie; Payne, Gregory F.; Bentley, William E.

    2014-08-01

    Microelectronic devices that contain biological components are typically used to interrogate biology rather than control biological function. Patterned assemblies of proteins and cells have, however, been used for in vitro metabolic engineering, where coordinated biochemical pathways allow cell metabolism to be characterized and potentially controlled on a chip. Such devices form part of technologies that attempt to recreate animal and human physiological functions on a chip and could be used to revolutionize drug development. These ambitious goals will, however, require new biofabrication methodologies that help connect microelectronics and biological systems and yield new approaches to device assembly and communication. Here, we report the electrically mediated assembly, interrogation and control of a multi-domain fusion protein that produces a bacterial signalling molecule. The biological system can be electrically tuned using a natural redox molecule, and its biochemical response is shown to provide the signalling cues to drive bacterial population behaviour. We show that the biochemical output of the system correlates with the electrical input charge, which suggests that electrical inputs could be used to control complex on-chip biological processes.

  6. Biochemical Characterization of the Phosphatase Domain of the Tumor Suppressor PH Domain Leucine-Rich Repeat Protein Phosphatase

    PubMed Central

    2015-01-01

    PH domain leucine-rich repeat protein phosphatase (PHLPP) directly dephosphorylates and inactivates Akt and protein kinase C and is therefore a prime target for pharmacological intervention of two key signaling pathways, the phosphatidylinositol 3-kinase and diacylglycerol signaling pathways. Here we report on the first biochemical characterization of the phosphatase domain of a PHLPP family member. The human PHLPP1 and PHLPP2 phosphatase domains were expressed and purified from bacteria or insect cells and their activities compared to that of full-length proteins immunoprecipitated from mammalian cells. Biochemical analyses reveal that the PHLPP phosphatase domain effectively dephosphorylates synthetic and peptidic substrates, that its activity is modulated by metals and lipophilic compounds, and that it has relatively high thermal stability. Mutational analysis of PHLPP2 reveals an unusual active site architecture compared to the canonical architecture of PP2C phosphatases and identifies key acidic residues (Asp 806, Glu 989, and Asp 1024) and bulky aromatic residues (Phe 783 and Phe 808) whose mutation impairs activity. Consistent with a unique active site architecture, we identify inhibitors that discriminate between PHLPP2 and PP2C?. These data establish PHLPP as a member of the PP2C family of phosphatases with a unique active site architecture. PMID:24892992

  7. Biochemical Phenotypes to Discriminate Microbial Subpopulations and Improve Outbreak Detection

    PubMed Central

    Galar, Alicia; Kulldorff, Martin; Rudnick, Wallis; O'Brien, Thomas F.; Stelling, John

    2013-01-01

    Background Clinical microbiology laboratories worldwide constitute an invaluable resource for monitoring emerging threats and the spread of antimicrobial resistance. We studied the growing number of biochemical tests routinely performed on clinical isolates to explore their value as epidemiological markers. Methodology/Principal Findings Microbiology laboratory results from January 2009 through December 2011 from a 793-bed hospital stored in WHONET were examined. Variables included patient location, collection date, organism, and 47 biochemical and 17 antimicrobial susceptibility test results reported by Vitek 2. To identify biochemical tests that were particularly valuable (stable with repeat testing, but good variability across the species) or problematic (inconsistent results with repeat testing), three types of variance analyses were performed on isolates of K. pneumonia: descriptive analysis of discordant biochemical results in same-day isolates, an average within-patient variance index, and generalized linear mixed model variance component analysis. Results: 4,200 isolates of K. pneumoniae were identified from 2,485 patients, 32% of whom had multiple isolates. The first two variance analyses highlighted SUCT, TyrA, GlyA, and GGT as “nuisance” biochemicals for which discordant within-patient test results impacted a high proportion of patient results, while dTAG had relatively good within-patient stability with good heterogeneity across the species. Variance component analyses confirmed the relative stability of dTAG, and identified additional biochemicals such as PHOS with a large between patient to within patient variance ratio. A reduced subset of biochemicals improved the robustness of strain definition for carbapenem-resistant K. pneumoniae. Surveillance analyses suggest that the reduced biochemical profile could improve the timeliness and specificity of outbreak detection algorithms. Conclusions The statistical approaches explored can improve the robust recognition of microbial subpopulations with routinely available biochemical test results, of value in the timely detection of outbreak clones and evolutionarily important genetic events. PMID:24391936

  8. Identifying, Assisting the Disturbed Adolescent.

    ERIC Educational Resources Information Center

    Carlson, Patricia L.; Schaefer, William

    1986-01-01

    Educators are in an excellent position to identify seriously troubled young people. Major causes of adolescent problems are discussed, including drugs, parental failure, and biochemical disturbances. Educators can best intervene by becoming aware of support services within their own school and community. (TE)

  9. Rescue of an in vitro neuron phenotype identified in Niemann-Pick disease, type C1 induced pluripotent stem cell-derived neurons by modulating the WNT pathway and calcium signaling.

    PubMed

    Efthymiou, Anastasia G; Steiner, Joe; Pavan, William J; Wincovitch, Stephen; Larson, Denise M; Porter, Forbes D; Rao, Mahendra S; Malik, Nasir

    2015-03-01

    Niemann-Pick disease, type C1 (NPC1) is a familial disorder that has devastating consequences on postnatal development with multisystem effects, including neurodegeneration. There is no Food and Drug Administration-approved treatment option for NPC1; however, several potentially therapeutic compounds have been identified in assays using yeast, rodent models, and NPC1 human fibroblasts. Although these discoveries were made in fibroblasts from NPC1 subjects and were in some instances validated in animal models of the disease, testing these drugs on a cell type more relevant for NPC1 neurological disease would greatly facilitate both study of the disease and identification of more relevant therapeutic compounds. Toward this goal, we have generated an induced pluripotent stem cell line from a subject homozygous for the most frequent NPC1 mutation (p.I1061T) and subsequently created a stable line of neural stem cells (NSCs). These NSCs were then used to create neurons as an appropriate disease model. NPC1 neurons display a premature cell death phenotype, and gene expression analysis of these cells suggests dysfunction of important signaling pathways, including calcium and WNT. The clear readout from these cells makes them ideal candidates for high-throughput screening and will be a valuable tool to better understand the development of NPC1 in neural cells, as well as to develop better therapeutic options for NPC1. PMID:25637190

  10. Genome-Wide siRNA Screen Identifies Complementary Signaling Pathways Involved in Listeria Infection and Reveals Different Actin Nucleation Mechanisms during Listeria Cell Invasion and Actin Comet Tail Formation

    PubMed Central

    Kühbacher, Andreas; Emmenlauer, Mario; Rämo, Pauli; Kafai, Natasha; Dehio, Christoph

    2015-01-01

    ABSTRACT Listeria monocytogenes enters nonphagocytic cells by a receptor-mediated mechanism that is dependent on a clathrin-based molecular machinery and actin rearrangements. Bacterial intra- and intercellular movements are also actin dependent and rely on the actin nucleating Arp2/3 complex, which is activated by host-derived nucleation-promoting factors downstream of the cell receptor Met during entry and by the bacterial nucleation-promoting factor ActA during comet tail formation. By genome-wide small interfering RNA (siRNA) screening for host factors involved in bacterial infection, we identified diverse cellular signaling networks and protein complexes that support or limit these processes. In addition, we could precise previously described molecular pathways involved in Listeria invasion. In particular our results show that the requirements for actin nucleators during Listeria entry and actin comet tail formation are different. Knockdown of several actin nucleators, including SPIRE2, reduced bacterial invasion while not affecting the generation of comet tails. Most interestingly, we observed that in contrast to our expectations, not all of the seven subunits of the Arp2/3 complex are required for Listeria entry into cells or actin tail formation and that the subunit requirements for each of these processes differ, highlighting a previously unsuspected versatility in Arp2/3 complex composition and function. PMID:25991686

  11. The energy costs of insulators in biochemical networks.

    PubMed

    Barton, John P; Sontag, Eduardo D

    2013-03-19

    Complex networks of biochemical reactions, such as intracellular protein signaling pathways and genetic networks, are often conceptualized in terms of modules--semiindependent collections of components that perform a well-defined function and which may be incorporated in multiple pathways. However, due to sequestration of molecular messengers during interactions and other effects, collectively referred to as retroactivity, real biochemical systems do not exhibit perfect modularity. Biochemical signaling pathways can be insulated from impedance and competition effects, which inhibit modularity, through enzymatic futile cycles that consume energy, typically in the form of ATP. We hypothesize that better insulation necessarily requires higher energy consumption. We test this hypothesis through a combined theoretical and computational analysis of a simplified physical model of covalent cycles, using two innovative measures of insulation, as well as a possible new way to characterize optimal insulation through the balancing of these two measures in a Pareto sense. Our results indicate that indeed better insulation requires more energy. While insulation may facilitate evolution by enabling a modular plug-and-play interconnection architecture, allowing for the creation of new behaviors by adding targets to existing pathways, our work suggests that this potential benefit must be balanced against the metabolic costs of insulation necessarily incurred in not affecting the behavior of existing processes. PMID:23528097

  12. Representations of metabolic knowledge: Pathways

    SciTech Connect

    Karp, P.D.; Paley, S.M. [SRI International, Menlo Park, CA (United States)

    1994-12-31

    The automatic generation of drawings of metabolic pathways is a challenging problem that depends intimately on exactly what information has been recorded for each pathway, and on how that information is encoded. The chief contributions of the paper are a minimized representation for biochemical pathways called the predecessor list, and inference procedures for converting the predecessor list into a pathway-graph representation that can serve as input to a pathway-drawing algorithm. The predecessor list has several advantages over the pathway graph, including its compactness and its lack of redundancy. The conversion between the two representations can be formulated as both a constraint-satisfaction problem and a logical inference problem, whose goal is to assign directions to reactions, and to determine which are the main chemical compounds in the reaction. We describe a set of production rules that solves this inference problem. We also present heuristics for inferring whether the exterior compounds that are substrates of reactions at the periphery of a pathway are side or main compounds. These techniques were evaluated on 18 metabolic pathways from the EcoCyc knowledge base.

  13. Representations of metabolic knowledge: pathways.

    PubMed

    Karp, P D; Paley, S M

    1994-01-01

    The automatic generation of drawings of metabolic pathways is a challenging problem that depends intimately on exactly what information has been recorded for each pathway, and on how that information is encoded. The chief contributions of the paper are a minimized representation for biochemical pathways called the predecessor list, and inference procedures for converting the predecessor list into a pathway-graph representation that can serve as input to a pathway-drawing algorithm. The predecessor list has several advantages over the pathway graph, including its compactness and its lack of redundancy. The conversion between the two representations can be formulated as both a constraint-satisfaction problem and a logical inference problem, whose goal is to assign directions to reactions, and to determine which are the main chemical compounds in the reaction. We describe a set of production rules that solves this inference problem. We also present heuristics for inferring whether the exterior compounds that are substrates of reactions at the periphery of a pathway are side or main compounds. These techniques were evaluated on 18 metabolic pathways from the EcoCyc knowledge base. PMID:7584392

  14. Misleading biochemical laboratory test results

    PubMed Central

    Nanji, Amin A.

    1984-01-01

    This article reviews the general and specific factors that interfere with the performance of common biochemical laboratory tests and the interpretation of their results. The clinical status of the patient, drug interactions, and in-vivo and in-vitro biochemical interactions and changes may alter the results obtained from biochemical analysis of blood constituents. Failure to recognize invalid laboratory test results may lead to injudicious and dangerous management of patients. PMID:6375845

  15. Two-Component Signal Transduction Pathways Regulating Growth and Cell Cycle Progression in a Bacterium: A System-Level Analysis

    PubMed Central

    2005-01-01

    Two-component signal transduction systems, comprised of histidine kinases and their response regulator substrates, are the predominant means by which bacteria sense and respond to extracellular signals. These systems allow cells to adapt to prevailing conditions by modifying cellular physiology, including initiating programs of gene expression, catalyzing reactions, or modifying protein–protein interactions. These signaling pathways have also been demonstrated to play a role in coordinating bacterial cell cycle progression and development. Here we report a system-level investigation of two-component pathways in the model organism Caulobacter crescentus. First, by a comprehensive deletion analysis we show that at least 39 of the 106 two-component genes are required for cell cycle progression, growth, or morphogenesis. These include nine genes essential for growth or viability of the organism. We then use a systematic biochemical approach, called phosphotransfer profiling, to map the connectivity of histidine kinases and response regulators. Combining these genetic and biochemical approaches, we identify a new, highly conserved essential signaling pathway from the histidine kinase CenK to the response regulator CenR, which plays a critical role in controlling cell envelope biogenesis and structure. Depletion of either cenK or cenR leads to an unusual, severe blebbing of cell envelope material, whereas constitutive activation of the pathway compromises cell envelope integrity, resulting in cell lysis and death. We propose that the CenK–CenR pathway may be a suitable target for new antibiotic development, given previous successes in targeting the bacterial cell wall. Finally, the ability of our in vitro phosphotransfer profiling method to identify signaling pathways that operate in vivo takes advantage of an observation that histidine kinases are endowed with a global kinetic preference for their cognate response regulators. We propose that this system-wide selectivity insulates two-component pathways from one another, preventing unwanted cross-talk. PMID:16176121

  16. Genetic analysis of photoreceptor action pathways in Arabidopsis thaliana. Progress report

    SciTech Connect

    Not Available

    1991-12-31

    The specific strategies and long-term goals of this proposal remain intact relative to the original proposal. We continue to isolate and characterize photomorphogenic mutants of Arabidopsis thaliana. The molecular and biochemical characterization of one of these mutants, det1, has led to one publication of original data and to one Society for Experimental Biology Symposium paper (see below). The phenotype of a second mutant, det2, has also been studied during this funding period. In addition, we have continued work on a general strategy to isolate mutations in trans-acting regulatory factors that mediate light-regulated gene expression, and have identified several potentially interesting regulatory mutants. In the third funding period, we will concentrate on the genetical, biochemical, and molecular characterization of these new mutants. Construction of double mutants between the new mutants and the previously characterized morphological mutants should allow us to construct a pathway for light-regulated seedling development in Arabidopsis.

  17. Simplification of biochemical models: a general approach based on the analysis of the impact of individual species and reactions on the systems dynamics

    PubMed Central

    2012-01-01

    Background Given the complex mechanisms underlying biochemical processes systems biology researchers tend to build ever increasing computational models. However, dealing with complex systems entails a variety of problems, e.g. difficult intuitive understanding, variety of time scales or non-identifiable parameters. Therefore, methods are needed that, at least semi-automatically, help to elucidate how the complexity of a model can be reduced such that important behavior is maintained and the predictive capacity of the model is increased. The results should be easily accessible and interpretable. In the best case such methods may also provide insight into fundamental biochemical mechanisms. Results We have developed a strategy based on the Computational Singular Perturbation (CSP) method which can be used to perform a "biochemically-driven" model reduction of even large and complex kinetic ODE systems. We provide an implementation of the original CSP algorithm in COPASI (a COmplex PAthway SImulator) and applied the strategy to two example models of different degree of complexity - a simple one-enzyme system and a full-scale model of yeast glycolysis. Conclusion The results show the usefulness of the method for model simplification purposes as well as for analyzing fundamental biochemical mechanisms. COPASI is freely available at http://www.copasi.org. PMID:22390191

  18. Thermodynamics of biochemical networks and duality theorems.

    PubMed

    De Martino, Daniele

    2013-05-01

    One interesting yet difficult computational issue has recently been posed in biophysics in regard to the implementation of thermodynamic constraints to complex networks. Biochemical networks of enzymes inside cells are among the most efficient, robust, differentiated, and flexible free-energy transducers in nature. How is the second law of thermodynamics encoded for these complex networks? In this article it is demonstrated that for chemical reaction networks in the steady state the exclusion (presence) of closed reaction cycles makes possible (impossible) the definition of a chemical potential vector. Interestingly, this statement is encoded in one of the key results in combinatorial optimization, i.e., the Gordan theorem of the alternatives. From a computational viewpoint, the theorem reveals that calculating a reaction's free energy and identifying infeasible loops in flux states are dual problems whose solutions are mutually exclusive, and this opens the way for efficient and scalable methods to perform the energy balance analysis of large-scale biochemical networks. PMID:23767488

  19. Insights into Ongoing Evolution of the Hexachlorocyclohexane Catabolic Pathway from Comparative Genomics of Ten Sphingomonadaceae Strains

    PubMed Central

    Pearce, Stephen L.; Oakeshott, John G.; Pandey, Gunjan

    2015-01-01

    Hexachlorocyclohexane (HCH), a synthetic organochloride, was first used as a broad-acre insecticide in the 1940s, and many HCH-degrading bacterial strains have been isolated from around the globe during the last 20 years. To date, the same degradation pathway (the lin pathway) has been implicated in all strains characterized, although the pathway has only been characterized intensively in two strains and for only a single HCH isomer. To further elucidate the evolution of the lin pathway, we have biochemically and genetically characterized three HCH-degrading strains from the Czech Republic and compared the genomes of these and seven other HCH-degrading bacterial strains. The three new strains each yielded a distinct set of metabolites during their degradation of HCH isomers. Variable assembly of the pathway is a common feature across the 10 genomes, eight of which (including all three Czech strains) were either missing key lin genes or containing duplicate copies of upstream lin genes (linA-F). The analysis also confirmed the important role of horizontal transfer mediated by insertion sequence IS6100 in the acquisition of the pathway, with a stronger association of IS6100 to the lin genes in the new strains. In one strain, a linA variant was identified that likely caused a novel degradation phenotype involving a shift in isomer preference. This study identifies a number of strains that are in the early stages of lin pathway acquisition and shows that the state of the pathway can explain the degradation patterns observed. PMID:25850427

  20. Molecular genetics of nucleotide sugar interconversion pathways in plants

    Microsoft Academic Search

    Wolf-Dieter Reiter; Gary F. Vanzin

    2001-01-01

    Nucleotide sugar interconversion pathways represent a series of enzymatic reactions by which plants synthesize activated monosaccharides for the incorporation into cell wall material. Although biochemical aspects of these metabolic pathways are reasonably well understood, the identification and characterization of genes encoding nucleotide sugar interconversion enzymes is still in its infancy. Arabidopsis mutants defective in the activation and interconversion of specific

  1. Mapping Circadian Output Pathways in Neurospora crassa 

    E-print Network

    Bennett, Lindsay Danielle

    2013-12-09

    . Our lab has focused on identifying output pathways from the clock, using the model organism Neurospora crassa. We have previously demonstrated the circadian regulation of the conserved Mitogen Activated Protein Kinase (MAPK) OS-2 pathway, a homolog...

  2. Narrative-based computational modelling of the Gp130/JAK/STAT signalling pathway

    PubMed Central

    Guerriero, Maria Luisa; Dudka, Anna; Underhill-Day, Nicholas; Heath, John K; Priami, Corrado

    2009-01-01

    Background Appropriately formulated quantitative computational models can support researchers in understanding the dynamic behaviour of biological pathways and support hypothesis formulation and selection by "in silico" experimentation. An obstacle to widespread adoption of this approach is the requirement to formulate a biological pathway as machine executable computer code. We have recently proposed a novel, biologically intuitive, narrative-style modelling language for biologists to formulate the pathway which is then automatically translated into an executable format and is, thus, usable for analysis via existing simulation techniques. Results Here we use a high-level narrative language in designing a computational model of the gp130/JAK/STAT signalling pathway and show that the model reproduces the dynamic behaviour of the pathway derived by biological observation. We then "experiment" on the model by simulation and sensitivity analysis to define those parameters which dominate the dynamic behaviour of the pathway. The model predicts that nuclear compartmentalisation and phosphorylation status of STAT are key determinants of the pathway and that alternative mechanisms of signal attenuation exert their influence on different timescales. Conclusion The described narrative model of the gp130/JAK/STAT pathway represents an interesting case study showing how, by using this approach, researchers can model biological systems without explicitly dealing with formal notations and mathematical expressions (typically used for biochemical modelling), nevertheless being able to obtain simulation and analysis results. We present the model and the sensitivity analysis results we have obtained, that allow us to identify the parameters which are most sensitive to perturbations. The results, which are shown to be in agreement with existing mathematical models of the gp130/JAK/STAT pathway, serve us as a form of validation of the model and of the approach itself. PMID:19368721

  3. Biochemical and Genetic Tests for Inhibitors of Leishmania Pteridine Pathways

    E-print Network

    Beverley, Stephen M.

    to methotrexate. We have proposed that the ability of PTR1 to serve as a metabolic bypass and thus modulate drug compound showed a methotrexate-like pattern of inhibition. Six compounds showed good inhibition resistance; engineered mutants; enzyme inhibitors; Leishmania; methotrexate; pteridine metabolism; pteridine

  4. A Competitive Stapled Peptide Screen Identifies a Selective Small Molecule that Overcomes MCL-1-dependent Leukemia Cell Survival

    PubMed Central

    Cohen, Nicole A.; Stewart, Michelle L.; Gavathiotis, Evripidis; Tepper, Jared L.; Bruekner, Susanne R.; Koss, Brian; Opferman, Joseph T.; Walensky, Loren D.

    2012-01-01

    SUMMARY Cancer cells hijack BCL-2 family survival proteins to suppress the death effectors and thereby enforce an immortal state. This is accomplished biochemically by an anti-apoptotic surface groove that neutralizes the pro-apoptotic BH3 ?-helix of death proteins. Anti-apoptotic MCL-1 in particular has emerged as a ubiquitous resistance factor in cancer. Whereas targeting the BCL-2 anti-apoptotic subclass effectively restores the death pathway in BCL-2-dependent cancer, the development of molecules tailored to the binding specificity of MCL-1 has lagged. We previously discovered that a hydrocarbon-stapled MCL-1 BH3 helix is an exquisitely selective MCL-1 antagonist. By deploying this unique reagent in a competitive screen, we identified an MCL-1 inhibitor molecule that selectively targets the BH3-binding groove of MCL-1, neutralizes its biochemical lockhold on apoptosis, and induces caspase activation and leukemia cell death in the specific context of MCL-1 dependence. PMID:22999885

  5. Dynamical modeling of the cholesterol regulatory pathway with Boolean networks

    PubMed Central

    Kervizic, Gwenael; Corcos, Laurent

    2008-01-01

    Background Qualitative dynamics of small gene regulatory networks have been studied in quite some details both with synchronous and asynchronous analysis. However, both methods have their drawbacks: synchronous analysis leads to spurious attractors and asynchronous analysis lacks computational efficiency, which is a problem to simulate large networks. We addressed this question through the analysis of a major biosynthesis pathway. Indeed the cholesterol synthesis pathway plays a pivotal role in dislypidemia and, ultimately, in cancer through intermediates such as mevalonate, farnesyl pyrophosphate and geranyl geranyl pyrophosphate, but no dynamic model of this pathway has been proposed until now. Results We set up a computational framework to dynamically analyze large biological networks. This framework associates a classical and computationally efficient synchronous Boolean analysis with a newly introduced method based on Markov chains, which identifies spurious cycles among the results of the synchronous simulation. Based on this method, we present here the results of the analysis of the cholesterol biosynthesis pathway and its physiological regulation by the Sterol Response Element Binding Proteins (SREBPs), as well as the modeling of the action of statins, inhibitor drugs, on this pathway. The in silico experiments show the blockade of the cholesterol endogenous synthesis by statins and its regulation by SREPBs, in full agreement with the known biochemical features of the pathway. Conclusion We believe that the method described here to identify spurious cycles opens new routes to compute large and biologically relevant models, thanks to the computational efficiency of synchronous simulation. Furthermore, to the best of our knowledge, we present here the first dynamic systems biology model of the human cholesterol pathway and several of its key regulatory control elements, hoping it would provide a good basis to perform in silico experiments and confront the resulting properties with published and experimental data. The model of the cholesterol pathway and its regulation, along with Boolean formulae used for simulation are available on our web site . Graphical results of the simulation are also shown online. The SBML model is available in the BioModels database with submission ID: MODEL0568648427. PMID:19025648

  6. An inventory of peroxisomal proteins and pathways in Drosophila melanogaster

    PubMed Central

    Faust, Joseph E.; Verma, Avani; Peng, Chengwei; McNew, James A.

    2012-01-01

    Peroxisomes are ubiquitous organelles housing a variety of essential biochemical pathways. Peroxisome dysfunction causes a spectrum of human diseases known as peroxisome biogenesis disorders (PBD). While much is known regarding the mechanism of peroxisome biogenesis, it is still unclear how peroxisome dysfunction leads to the disease state. Several recent studies have shown that mutations in Drosophila peroxin genes cause phenotypes similar to those seen in humans with PBDs suggesting that Drosophila might be a useful system to model PBDs. We have analyzed the proteome of Drosophila to identify the proteins involved in peroxisomal biogenesis and homeostasis as well as metabolic enzymes that function within the organelle. The subcellular localization of five of these predicted peroxisomal proteins was confirmed. Similar to C. elegans, Drosophila appears to only utilize the peroxisome targeting signal (PTS) type 1 system for matrix protein import. This work will further our understanding of peroxisomes in Drosophila and add to the usefulness of this emerging model system. PMID:22758915

  7. Station Identifier

    Microsoft Academic Search

    J. Stepan

    1968-01-01

    This paper describes an end office tributary identifier which sends to a toll center the calling subscriber's directory number. It is arranged to interface with the Bell System's centralized automatic message accounting (CAMA) centers. The electronic identifier operates on either a terminal per line, a terminal per station, or mixed basis. In operating, it feeds an ac signal on the

  8. Inferring branching pathways in genome-scale metabolic networks

    Microsoft Academic Search

    Esa Pitkänen; Paula Jouhten; Juho Rousu

    2009-01-01

    BACKGROUND: A central problem in computational metabolic modelling is how to find biochemically plausible pathways between metabolites in a metabolic network. Two general, complementary frameworks have been utilized to find metabolic pathways: constraint-based modelling and graph-theoretical path finding approaches. In constraint-based modelling, one aims to find pathways where metabolites are balanced in a pseudo steady-state. Constraint-based methods, such as elementary

  9. A Course in... Biochemical Engineering.

    ERIC Educational Resources Information Center

    Ng, Terry K-L.; And Others

    1988-01-01

    Describes a chemical engineering course for senior undergraduates and first year graduate students in biochemical engineering. Discusses five experiments used in the course: aseptic techniques, dissolved oxygen measurement, oxygen uptake by yeast, continuous sterilization, and cultivation of microorganisms. (MVL)

  10. The Tor Pathway Regulates Gene Expression by Linking Nutrient Sensing to Histone Acetylation

    PubMed Central

    Rohde, John R.; Cardenas, Maria E.

    2003-01-01

    The Tor pathway mediates cell growth in response to nutrient availability, in part by inducing ribosomal protein (RP) gene expression via an unknown mechanism. Expression of RP genes coincides with recruitment of the Esa1 histone acetylase to RP gene promoters. We show that inhibition of Tor with rapamycin releases Esa1 from RP gene promoters and leads to histone H4 deacetylation without affecting promoter occupancy by Rap1 and Abf1. Genetic and biochemical evidence identifies Rpd3 as the major histone deacetylase responsible for reversing histone H4 acetylation at RP gene promoters in response to Tor inhibition by rapamycin or nutrient limitation. Our results illustrate that the Tor pathway links nutrient sensing with histone acetylation to control RP gene expression and cell growth. PMID:12509460

  11. Biochemical changes of ischemia.

    PubMed

    Levitsky, S; Feinberg, H

    1975-07-01

    Normothermic ischemic arrest by aortic cross-clamping, a widely used clinical technique, is associated with metabolic changes in the myocardium that are incompletely understood. The effects of aortic cross-clamping on glycolytic pathways as well as associated morphological changes are discussed. Emphasis is placed on the conservation of high-energy phosphate moieties during the period of cross-clamping as well as during reperfusion. A marked reduction in total high-energy phosphates (62%) and glycogen (63%) and an increase in lactate production (243%) denote a shift to anaerobic metabolism during the period of arrest. Despite reperfusion, total high-energy nucleotides remained depressed. The data suggest that persistent abnormal myocardial carbohydrate metabolism and low levels of high-energy nucleotides prevent recovery of contractility following normothermic ischemic arrest and reperfusion. PMID:803171

  12. Evidence for the Existence in Arabidopsis thaliana of the Proteasome Proteolytic Pathway

    PubMed Central

    Polge, Cécile; Jaquinod, Michel; Holzer, Frances; Bourguignon, Jacques; Walling, Linda; Brouquisse, Renaud

    2009-01-01

    Heavy metals are known to generate reactive oxygen species that lead to the oxidation and fragmentation of proteins, which become toxic when accumulated in the cell. In this study, we investigated the role of the proteasome during cadmium stress in the leaves of Arabidopsis thaliana plants. Using biochemical and proteomics approaches, we present the first evidence of an active proteasome pathway in plants. We identified and characterized the peptidases acting sequentially downstream from the proteasome in animal cells as follows: tripeptidyl-peptidase II, thimet oligopeptidase, and leucine aminopeptidase. We investigated the proteasome proteolytic pathway response in the leaves of 6-week-old A. thaliana plants grown hydroponically for 24, 48, and 144 h in the presence or absence of 50 ?m cadmium. The gene expression and proteolytic activity of the proteasome and the different proteases of the pathway were found to be up-regulated in response to cadmium. In an in vitro assay, oxidized bovine serum albumin and lysozyme were more readily degraded in the presence of 20 S proteasome and tripeptidyl-peptidase II than their nonoxidized form, suggesting that oxidized proteins are preferentially degraded by the Arabidopsis 20 S proteasome pathway. These results show that, in response to cadmium, the 20 S proteasome proteolytic pathway is up-regulated at both RNA and activity levels in Arabidopsis leaves and may play a role in degrading oxidized proteins generated by the stress. PMID:19822524

  13. Determination of antifungal, biochemical and physiological features of Trichoderma koningiopsis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Trichoderma koningiopsis is a species that has been recently identified and has not yet been published, but is in press. Due to the absence of reported data on this species, antifungal, biochemical and physiological features were analyzed for the Trichoderma koningiopsis strain isolated from root se...

  14. MATLAB-Based Teaching Modules in Biochemical Engineering

    ERIC Educational Resources Information Center

    Lee, Kilho; Comolli, Noelle K.; Kelly, William J.; Huang, Zuyi

    2015-01-01

    Mathematical models play an important role in biochemical engineering. For example, the models developed in the field of systems biology have been used to identify drug targets to treat pathogens such as Pseudomonas aeruginosa in biofilms. In addition, competitive binding models for chromatography processes have been developed to predict expanded…

  15. Chris Moore Biochem 218

    E-print Network

    as well studied as E. coli. Despite these challenges, several groups have recently made an effort to produce methods of computationally identifying various classes of sRNA genes in E. coli. They have used in E. coli. The three major computational methods of sRNA gene-finding used by the four groups

  16. Exploring biological electron transfer pathway dynamics with the Pathways plugin for VMD.

    PubMed

    Balabin, Ilya A; Hu, Xiangqian; Beratan, David N

    2012-03-30

    We describe the new Pathways plugin for the molecular visualization program visual molecular dynamics. The plugin identifies and visualizes tunneling pathways and pathway families in biomolecules, and calculates relative electronic couplings. The plugin includes unique features to estimate the importance of individual atoms for mediating the coupling, to analyze the coupling sensitivity to thermal motion, and to visualize pathway fluctuations. The Pathways plugin is open source software distributed under the terms of the GNU's Not Unix (GNU) public license. PMID:22298319

  17. Exploring Biological Electron Transfer Pathway Dynamics with the Pathways Plugin for VMD

    PubMed Central

    Balabin, Ilya A.; Hu, Xiangqian; Beratan, David N.

    2012-01-01

    We describe the new Pathways plugin for the molecular visualization program VMD. The plugin identifies and visualizes tunneling pathways and pathway families in biomolecules and calculates relative electronic couplings. The plugin includes unique features to estimate the importance of individual atoms for mediating the coupling, to analyze the coupling sensitivity to thermal motion, and to visualize pathway fluctuations. The Pathways plugin is open source software distributed under the terms of the GNU public license. PMID:22298319

  18. Biochemical markers of spontaneous preterm birth in asymptomatic women.

    PubMed

    Chan, Ronna L

    2014-01-01

    Preterm birth is a delivery that occurs at less than 37 completed weeks of gestation and it is associated with perinatal morbidity and mortality. Spontaneous preterm birth accounts for up to 75% of all preterm births. A number of maternal or fetal characteristics have been associated with preterm birth, but the use of individual or group biochemical markers have advanced some of the understanding on the mechanisms leading to spontaneous preterm birth. This paper provides a summary on the current literature on the use of biochemical markers in predicting spontaneous preterm birth in asymptomatic women. Evidence from the literature suggests fetal fibronectin, cervical interleukin-6, and ?-fetoprotein as promising biochemical markers in predicting spontaneous preterm birth in asymptomatic women. The role of gene-gene and gene-environment interactions, as well as epigenetics, has the potential to further elucidate and improve understanding of the underlying mechanisms or pathways of spontaneous preterm birth. Refinement in study design and methodology is needed in future research for the development and validation of individual or group biochemical marker(s) for use independently or in conjunction with other potential risk factors such as genetic variants and environmental and behavioral factors in predicting spontaneous preterm birth across diverse populations. PMID:24551837

  19. Identifying Erosion

    NSDL National Science Digital Library

    COSI

    2009-01-01

    In this environmental science activity (page 3 of the PDF), leaners will identify and explain the causes of erosion. They will observe the effects of erosion on the surrounding area and further explore examples of erosion online. An extension activity allows learners to make a hands-on model of soil erosion. Though this was created as a pre-visit activity for a workshop about water flow and erosion, it makes a great stand-alone activity as well!

  20. Identify Symmetry

    NSDL National Science Digital Library

    Mrs. Neubert

    2011-03-03

    This unit will teach you how to identify symmetry in everyday objects and mathematical shapes in lines and rotational symmetry. What is line symmetry? Click on the link to find out: Line Symmetry Here is a line activity to see if you understand it: Line Symmetry Class Zone See if you understand the concepts by doing the following quiz: Line Symmetry Work Now for rotational symmetry: Rotational Symmetry See if you understand rotational symmetry by taking this quiz: Rotational Symmetry Work ...

  1. Predicted efficacy of the Palestinian wheat flour fortification program: complementary analysis of biochemical and dietary data

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Objective: To utilize complementary biochemical and dietary data collected before the initiation of national flour fortification to 1) identify micronutrient insufficiencies or deficiencies and dietary inadequacies in Palestinian women and children in vulnerable communities and 2) assess the suitabi...

  2. Pattern selection by dynamical biochemical signals.

    PubMed

    Palau-Ortin, David; Formosa-Jordan, Pau; Sancho, José M; Ibañes, Marta

    2015-03-24

    The development of multicellular organisms involves cells to decide their fate upon the action of biochemical signals. This decision is often spatiotemporally coordinated such that a spatial pattern arises. The dynamics that drive pattern formation usually involve genetic nonlinear interactions and positive feedback loops. These complex dynamics may enable multiple stable patterns for the same conditions. Under these circumstances, pattern formation in a developing tissue involves a selection process: why is a certain pattern formed and not another stable one? Herein we computationally address this issue in the context of the Notch signaling pathway. We characterize a dynamical mechanism for developmental selection of a specific pattern through spatiotemporal changes of the control parameters of the dynamics, in contrast to commonly studied situations in which initial conditions and noise determine which pattern is selected among multiple stable ones. This mechanism can be understood as a path along the parameter space driven by a sequence of biochemical signals. We characterize the selection process for three different scenarios of this dynamical mechanism that can take place during development: the signal either 1) acts in all the cells at the same time, 2) acts only within a cluster of cells, or 3) propagates along the tissue. We found that key elements for pattern selection are the destabilization of the initial pattern, the subsequent exploration of other patterns determined by the spatiotemporal symmetry of the parameter changes, and the speeds of the path compared to the timescales of the pattern formation process itself. Each scenario enables the selection of different types of patterns and creates these elements in distinct ways, resulting in different features. Our approach extends the concept of selection involved in cellular decision-making, usually applied to cell-autonomous decisions, to systems that collectively make decisions through cell-to-cell interactions. PMID:25809268

  3. Biochemical characterisation during seed development of oil palm (Elaeis guineensis).

    PubMed

    Kok, Sau-Yee; Namasivayam, Parameswari; Ee, Gwendoline Cheng-Lian; Ong-Abdullah, Meilina

    2013-07-01

    Developmental biochemical information is a vital base for the elucidation of seed physiology and metabolism. However, no data regarding the biochemical profile of oil palm (Elaeis guineensis Jacq.) seed development has been reported thus far. In this study, the biochemical changes in the developing oil palm seed were investigated to study their developmental pattern. The biochemical composition found in the seed differed significantly among the developmental stages. During early seed development, the water, hexose (glucose and fructose), calcium and manganese contents were present in significantly high levels compared to the late developmental stage. Remarkable changes in the biochemical composition were observed at 10 weeks after anthesis (WAA): the dry weight and sucrose content increased significantly, whereas the water content and hexose content declined. The switch from a high to low hexose/sucrose ratio could be used to identify the onset of the maturation phase. At the late stage, dramatic water loss occurred, whereas the content of storage reserves increased progressively. Lauric acid was the most abundant fatty acid found in oil palm seed starting from 10 WAA. PMID:23575803

  4. Genetic study and further biochemical characterization of a tobacco mutant that overproduces sterols

    Microsoft Academic Search

    Pascale Maillot-Vernier; Laurence Gondet; Hubert Schaller; Pierre Benveniste; Geneviève Belliard

    1991-01-01

    A genetic and biochemical characterization is presented of a tobacco mutant that was previously shown to have an increased sterol content with an accumulation of biosynthetic intermediates. We first show that a precise regulation of the membrane sterol composition occurs in this mutant, via a selective esterification process. Indeed, sterols representing the usual end-products of the biosynthetic pathway are preferably

  5. A comprehensive urinary metabolomic approach for identifying kidney cancer

    Microsoft Academic Search

    Tobias Kind; Vladimir Tolstikov; Oliver Fiehn; Robert H. Weiss

    2007-01-01

    The diagnosis of cancer by examination of the urine has the potential to improve patient outcomes by means of earlier detection. Due to the fact that the urine contains metabolic signatures of many biochemical pathways, this biofluid is ideally suited for metabolomic analysis, especially involving diseases of the kidney and urinary system. In this pilot study, we test three independent

  6. Biochemical Features and Functional Implications of the RNA-Based T-Box Regulatory Mechanism

    PubMed Central

    Gutiérrez-Preciado, Ana; Henkin, Tina M.; Grundy, Frank J.; Yanofsky, Charles; Merino, Enrique

    2009-01-01

    Summary: The T-box mechanism is a common regulatory strategy used for modulating the expression of genes of amino acid metabolism-related operons in gram-positive bacteria, especially members of the Firmicutes. T-box regulation is usually based on a transcription attenuation mechanism in which an interaction between a specific uncharged tRNA and the 5? region of the transcript stabilizes an antiterminator structure in preference to a terminator structure, thereby preventing transcription termination. Although single T-box regulatory elements are common, double or triple T-box arrangements are also observed, expanding the regulatory range of these elements. In the present study, we predict the functional implications of T-box regulation in genes encoding aminoacyl-tRNA synthetases, proteins of amino acid biosynthetic pathways, transporters, and regulatory proteins. We also consider the global impact of the use of this regulatory mechanism on cell physiology. Novel biochemical relationships between regulated genes and their corresponding metabolic pathways were revealed. Some of the genes identified, such as the quorum-sensing gene luxS, in members of the Lactobacillaceae were not previously predicted to be regulated by the T-box mechanism. Our analyses also predict an imbalance in tRNA sensing during the regulation of operons containing multiple aminoacyl-tRNA synthetase genes or biosynthetic genes involved in pathways common to more than one amino acid. Based on the distribution of T-box regulatory elements, we propose that this regulatory mechanism originated in a common ancestor of members of the Firmicutes, Chloroflexi, Deinococcus-Thermus group, and Actinobacteria and was transferred into the Deltaproteobacteria by horizontal gene transfer. PMID:19258532

  7. Pathway Analysis

    Cancer.gov

    Projects such as The Cancer Genome Atlas have gathered enormous quantities of data from human tumor samples. Informaticians at the National Lab are looking within such data for insights about the influence of mutant RAS genes on signaling pathways in cancers. On a smaller scale, the RAS Initiative will use numerous experimental platforms to interrogate cell lines expressing mutant RAS genes.

  8. Targeting the PI3-kinase/Akt/mTOR Signaling Pathway

    PubMed Central

    Hassan, Burhan; Akcakanat, Argun; Holder, Ashley M.; Meric-Bernstam, Funda

    2013-01-01

    Synopsis This article presents an overview of the PI3K/Akt/mTOR signaling pathway. As a central regulator of cell growth, protein translation, survival, and metabolism, activation of this signaling pathway contributes to the pathogenesis of many tumor types. Biochemical and genetic aberrations of this pathway observed in various cancer types will be explored. Lastly, pathway inhibitors both in development and already FDA-approved will be discussed. PMID:24012393

  9. Identifying Species

    NSDL National Science Digital Library

    Michael DiSpezio

    This two part activity will allow students to investigate biological diversity in the area of their school. They will first prepare a taxonomic key to distinguish between the four insects or spiders that they have selected. All of the keys are combined and students then perform a transect study of a neighborhood field or school playing ground. Finally as a class students will compile a list of the animals and plants that are found within a mile of their school. They may need to use field guides, local resources, taxonomic keys, and species lists to help identify these organisms. Once they have compiled their list they will organize the species into the taxonomic groups they have studied.

  10. Acute overdose with levodopa. Clinical and biochemical consequences.

    PubMed

    Hoehn, M M; Rutledge, C O

    1975-08-01

    A 61-year-old parkinsonian patient ingested up to 100 gm of levodopa during a period of 12 hours. Signs of parkinsonism were completely alleviated. Adverse effects included initial hypertension followed rapidly by hypotension of a few hours' duration, prolonged symptomatic postural hypotension, sinus tachycardia, mental confusion, insomnia, and anorexia. The effects of the overdose gradually subsided over 1 week. Analyses of serum and urine for dopa and its metabolites confirmed the overdose, which biochemically resulted in apparent saturation of two enzymatic pathways that inactivate dopamine: conjugation with sulfuric acid and O-methylation. PMID:1171416

  11. Metabolic Engineering to Develop a Pathway for the Selective Cleavage of Carbon-Nitrogen Bonds

    SciTech Connect

    John J. Kilbane II

    2005-10-01

    The objective of the project is to develop a biochemical pathway for the selective cleavage of C-N bonds in molecules found in petroleum. Specifically a novel biochemical pathway will be developed for the selective cleavage of C-N bonds in carbazole. The cleavage of the first C-N bond in carbazole is accomplished by the enzyme carbazole dioxygenase, that catalyzes the conversion of carbazole to 2-aminobiphenyl-2,3-diol. The genes encoding carbazole dioxygenase were cloned from Sphingomonas sp. GTIN11 and from Pseudomonas resinovorans CA10. The selective cleavage of the second C-N bond has been challenging, and efforts to overcome that challenge have been the focus of recent research in this project. Enrichment culture experiments succeeded in isolating bacterial cultures that can metabolize 2-aminobiphenyl, but no enzyme capable of selectively cleaving the C-N bond in 2-aminobiphenyl has been identified. Aniline is very similar to the structure of 2-aminobiphenyl and aniline dioxygenase catalyzes the conversion of aniline to catechol and ammonia. For the remainder of the project the emphasis of research will be to simultaneously express the genes for carbazole dioxygenase and for aniline dioxygenase in the same bacterial host and then to select for derivative cultures capable of using carbazole as the sole source of nitrogen.

  12. The Hippo Signaling Pathway Interactome

    PubMed Central

    Kwon, Young; Vinayagam, Arunachalam; Sun, Xiaoyun; Dephoure, Noah; Gygi, Steven P.; Hong, Pengyu; Perrimon, Norbert

    2014-01-01

    The Hippo pathway controls metazoan organ growth by regulating cell proliferation and apoptosis. Many components have been identified, but our knowledge of the composition and structure of this pathway is still incomplete. Using existing pathway components as baits, we generated by mass spectrometry a high-confidence Drosophila Hippo protein-protein interaction network (Hippo-PPIN) consisting of 153 proteins and 204 interactions. Depletion of 67% of the proteins by RNA interference regulated the transcriptional coactivator Yorkie (Yki) either positively or negatively. We selected for further characterization a new member of the alpha-arrestin family, Leash, and show that it promotes degradation of Yki through the lysosomal pathway. Given the importance of the Hippo pathway in tumor development, the Hippo-PPIN will contribute to our understanding of this network in both normal growth and cancer. PMID:24114784

  13. A novel pathway combining calreticulin exposure and ATP secretion in immunogenic cancer cell death

    PubMed Central

    Garg, Abhishek D; Krysko, Dmitri V; Verfaillie, Tom; Kaczmarek, Agnieszka; Ferreira, Gabriela B; Marysael, Thierry; Rubio, Noemi; Firczuk, Malgorzata; Mathieu, Chantal; Roebroek, Anton J M; Annaert, Wim; Golab, Jakub; de Witte, Peter; Vandenabeele, Peter; Agostinis, Patrizia

    2012-01-01

    Surface-exposed calreticulin (ecto-CRT) and secreted ATP are crucial damage-associated molecular patterns (DAMPs) for immunogenic apoptosis. Inducers of immunogenic apoptosis rely on an endoplasmic reticulum (ER)-based (reactive oxygen species (ROS)-regulated) pathway for ecto-CRT induction, but the ATP secretion pathway is unknown. We found that after photodynamic therapy (PDT), which generates ROS-mediated ER stress, dying cancer cells undergo immunogenic apoptosis characterized by phenotypic maturation (CD80high, CD83high, CD86high, MHC-IIhigh) and functional stimulation (NOhigh, IL-10absent, IL-1?high) of dendritic cells as well as induction of a protective antitumour immune response. Intriguingly, early after PDT the cancer cells displayed ecto-CRT and secreted ATP before exhibiting biochemical signatures of apoptosis, through overlapping PERK-orchestrated pathways that require a functional secretory pathway and phosphoinositide 3-kinase (PI3K)-mediated plasma membrane/extracellular trafficking. Interestingly, eIF2? phosphorylation and caspase-8 signalling are dispensable for this ecto-CRT exposure. We also identified LRP1/CD91 as the surface docking site for ecto-CRT and found that depletion of PERK, PI3K p110? and LRP1 but not caspase-8 reduced the immunogenicity of the cancer cells. These results unravel a novel PERK-dependent subroutine for the early and simultaneous emission of two critical DAMPs following ROS-mediated ER stress. PMID:22252128

  14. A novel pathway combining calreticulin exposure and ATP secretion in immunogenic cancer cell death.

    PubMed

    Garg, Abhishek D; Krysko, Dmitri V; Verfaillie, Tom; Kaczmarek, Agnieszka; Ferreira, Gabriela B; Marysael, Thierry; Rubio, Noemi; Firczuk, Malgorzata; Mathieu, Chantal; Roebroek, Anton J M; Annaert, Wim; Golab, Jakub; de Witte, Peter; Vandenabeele, Peter; Agostinis, Patrizia

    2012-03-01

    Surface-exposed calreticulin (ecto-CRT) and secreted ATP are crucial damage-associated molecular patterns (DAMPs) for immunogenic apoptosis. Inducers of immunogenic apoptosis rely on an endoplasmic reticulum (ER)-based (reactive oxygen species (ROS)-regulated) pathway for ecto-CRT induction, but the ATP secretion pathway is unknown. We found that after photodynamic therapy (PDT), which generates ROS-mediated ER stress, dying cancer cells undergo immunogenic apoptosis characterized by phenotypic maturation (CD80(high), CD83(high), CD86(high), MHC-II(high)) and functional stimulation (NO(high), IL-10(absent), IL-1?(high)) of dendritic cells as well as induction of a protective antitumour immune response. Intriguingly, early after PDT the cancer cells displayed ecto-CRT and secreted ATP before exhibiting biochemical signatures of apoptosis, through overlapping PERK-orchestrated pathways that require a functional secretory pathway and phosphoinositide 3-kinase (PI3K)-mediated plasma membrane/extracellular trafficking. Interestingly, eIF2? phosphorylation and caspase-8 signalling are dispensable for this ecto-CRT exposure. We also identified LRP1/CD91 as the surface docking site for ecto-CRT and found that depletion of PERK, PI3K p110? and LRP1 but not caspase-8 reduced the immunogenicity of the cancer cells. These results unravel a novel PERK-dependent subroutine for the early and simultaneous emission of two critical DAMPs following ROS-mediated ER stress. PMID:22252128

  15. MAPKs in development: insights from Dictyostelium signaling pathways

    PubMed Central

    Hadwiger, Jeffrey A.; Nguyen, Hoai-Nghia

    2011-01-01

    Mitogen activated protein kinases (MAPKs) play important roles in the development of eukaryotic organisms through the regulation of signal transduction pathways stimulated by external signals. MAPK signaling pathways have been associated with the regulation of cell growth, differentiation, and chemotaxis, indicating MAPKs contribute to a diverse set of developmental processes. In most eukaryotes, the diversity of external signals is likely to far exceed the diversity of MAPKs, suggesting that multiple signaling pathways might share MAPKs. Do different signaling pathways converge before MAPK function or can MAPKs maintain signaling specificity through interactions with specific proteins? The genetic and biochemical analysis of MAPK pathways in simple eukaryotes such as Dictyostelium offers opportunities to investigate functional specificity of MAPKs in G protein-mediated signal transduction pathways. This review considers the regulation and specificity of MAPK function in pathways that control Dictyostelium growth and development. PMID:21666837

  16. UHRF1 is a sensor for DNA interstrand crosslinks and recruits FANCD2 to initiate the Fanconi anemia pathway.

    PubMed

    Liang, Chih-Chao; Zhan, Bao; Yoshikawa, Yasunaga; Haas, Wilhelm; Gygi, Steven P; Cohn, Martin A

    2015-03-31

    The Fanconi anemia (FA) pathway is critical for the cellular response to toxic DNA interstrand crosslinks (ICLs). Using a biochemical purification strategy, we identified UHRF1 as a protein that specifically interacts with ICLs in vitro and in vivo. Reduction of cellular levels of UHRF1 by RNAi attenuates the FA pathway and sensitizes cells to mitomycin C. Knockdown cells display a drastic reduction in FANCD2 foci formation. Using live-cell imaging, we observe that UHRF1 is rapidly recruited to chromatin in response to DNA crosslinking agents and that this recruitment both precedes and is required for the recruitment of FANCD2 to ICLs. Based on these results, we describe a mechanism of ICL sensing and propose that UHRF1 is a critical factor that binds to ICLs. In turn, this binding is necessary for the subsequent recruitment of FANCD2, which allows the DNA repair process to initiate. PMID:25801034

  17. Feeding and Fasting Signals Converge on the LKB1-SIK3 Pathway to Regulate Lipid Metabolism in Drosophila

    PubMed Central

    Choi, Sekyu; Lim, Dae-Sik; Chung, Jongkyeong

    2015-01-01

    LKB1 plays important roles in governing energy homeostasis by regulating AMP-activated protein kinase (AMPK) and other AMPK-related kinases, including the salt-inducible kinases (SIKs). However, the roles and regulation of LKB1 in lipid metabolism are poorly understood. Here we show that Drosophila LKB1 mutants display decreased lipid storage and increased gene expression of brummer, the Drosophila homolog of adipose triglyceride lipase (ATGL). These phenotypes are consistent with those of SIK3 mutants and are rescued by expression of constitutively active SIK3 in the fat body, suggesting that SIK3 is a key downstream kinase of LKB1. Using genetic and biochemical analyses, we identify HDAC4, a class IIa histone deacetylase, as a lipolytic target of the LKB1-SIK3 pathway. Interestingly, we found that the LKB1-SIK3-HDAC4 signaling axis is modulated by dietary conditions. In short-term fasting, the adipokinetic hormone (AKH) pathway, related to the mammalian glucagon pathway, inhibits the kinase activity of LKB1 as shown by decreased SIK3 Thr196 phosphorylation, and consequently induces HDAC4 nuclear localization and brummer gene expression. However, under prolonged fasting conditions, AKH-independent signaling decreases the activity of the LKB1-SIK3 pathway to induce lipolytic responses. We also identify that the Drosophila insulin-like peptides (DILPs) pathway, related to mammalian insulin pathway, regulates SIK3 activity in feeding conditions independently of increasing LKB1 kinase activity. Overall, these data suggest that fasting stimuli specifically control the kinase activity of LKB1 and establish the LKB1-SIK3 pathway as a converging point between feeding and fasting signals to control lipid homeostasis in Drosophila. PMID:25996931

  18. Feeding and Fasting Signals Converge on the LKB1-SIK3 Pathway to Regulate Lipid Metabolism in Drosophila.

    PubMed

    Choi, Sekyu; Lim, Dae-Sik; Chung, Jongkyeong

    2015-05-01

    LKB1 plays important roles in governing energy homeostasis by regulating AMP-activated protein kinase (AMPK) and other AMPK-related kinases, including the salt-inducible kinases (SIKs). However, the roles and regulation of LKB1 in lipid metabolism are poorly understood. Here we show that Drosophila LKB1 mutants display decreased lipid storage and increased gene expression of brummer, the Drosophila homolog of adipose triglyceride lipase (ATGL). These phenotypes are consistent with those of SIK3 mutants and are rescued by expression of constitutively active SIK3 in the fat body, suggesting that SIK3 is a key downstream kinase of LKB1. Using genetic and biochemical analyses, we identify HDAC4, a class IIa histone deacetylase, as a lipolytic target of the LKB1-SIK3 pathway. Interestingly, we found that the LKB1-SIK3-HDAC4 signaling axis is modulated by dietary conditions. In short-term fasting, the adipokinetic hormone (AKH) pathway, related to the mammalian glucagon pathway, inhibits the kinase activity of LKB1 as shown by decreased SIK3 Thr196 phosphorylation, and consequently induces HDAC4 nuclear localization and brummer gene expression. However, under prolonged fasting conditions, AKH-independent signaling decreases the activity of the LKB1-SIK3 pathway to induce lipolytic responses. We also identify that the Drosophila insulin-like peptides (DILPs) pathway, related to mammalian insulin pathway, regulates SIK3 activity in feeding conditions independently of increasing LKB1 kinase activity. Overall, these data suggest that fasting stimuli specifically control the kinase activity of LKB1 and establish the LKB1-SIK3 pathway as a converging point between feeding and fasting signals to control lipid homeostasis in Drosophila. PMID:25996931

  19. Oscillatory Dynamics of the Extracellular Signal-regulated Kinase Pathway

    SciTech Connect

    Shankaran, Harish; Wiley, H. S.

    2010-12-01

    The extracellular signal-regulated kinase (ERK) pathway is a central signaling pathway in development and disease and is regulated by multiple negative and positive feedback loops. Recent studies have shown negative feedback from ERK to upstream regulators can give rise to biochemical oscillations with a periodicity of between 15-30 minutes. Feedback due to the stimulated transcription of negative regulators of the ERK pathway can also give rise to transcriptional oscillations with a periodicity of 1-2h. The biological significance of these oscillations is not clear, but recent evidence suggests that transcriptional oscillations participate in developmental processes, such as somite formation. Biochemical oscillations are more enigmatic, but could provide a mechanism for encoding different types of inputs into a common signaling pathway.

  20. Biochemical and genetic insights into asukamycin biosynthesis.

    PubMed

    Rui, Zhe; Petrícková, Katerina; Skanta, Frantisek; Pospísil, Stanislav; Yang, Yanling; Chen, Chung-Yung; Tsai, Shih-Feng; Floss, Heinz G; Petrícek, Miroslav; Yu, Tin-Wein

    2010-08-01

    Asukamycin, a member of the manumycin family metabolites, is an antimicrobial and potential antitumor agent isolated from Streptomyces nodosus subsp. asukaensis. The entire asukamycin biosynthetic gene cluster was cloned, assembled, and expressed heterologously in Streptomyces lividans. Bioinformatic analysis and mutagenesis studies elucidated the biosynthetic pathway at the genetic and biochemical level. Four gene sets, asuA-D, govern the formation and assembly of the asukamycin building blocks: a 3-amino-4-hydroxybenzoic acid core component, a cyclohexane ring, two triene polyketide chains, and a 2-amino-3-hydroxycyclopent-2-enone moiety to form the intermediate protoasukamycin. AsuE1 and AsuE2 catalyze the conversion of protoasukamycin to 4-hydroxyprotoasukamycin, which is epoxidized at C5-C6 by AsuE3 to the final product, asukamycin. Branched acyl CoA starter units, derived from Val, Leu, and Ile, can be incorporated by the actions of the polyketide synthase III (KSIII) AsuC3/C4 as well as the cellular fatty acid synthase FabH to produce the asukamycin congeners A2-A7. In addition, the type II thioesterase AsuC15 limits the cellular level of omega-cyclohexyl fatty acids and likely maintains homeostasis of the cellular membrane. PMID:20522559

  1. External physical and biochemical stimulation to enhance skeletal muscle bioengineering

    PubMed Central

    Plock, Jan; Eberli, Daniel

    2015-01-01

    Purpose of review Cell based muscle tissue engineering carries the potential to revert the functional loss of muscle tissue caused by disease and trauma. Although muscle tissue can be bioengineered using various precursor cells, major limitations still remain. Recent findings In the last decades several cellular pathways playing a crucial role in muscle tissue regeneration have been described. These pathways can be influenced by external stimuli and they not only orchestrate the regenerative process after physiologic wear and muscle trauma, but they also play an important part in aging and maintaining the stem cell niche, which is required to maintain long-term muscle function. Summary In this review article we will highlight possible new avenues using external physical and biochemical stimulation in order to optimize muscle bioengineering. PMID:25453267

  2. Regulatory Network of Secondary Metabolism in Brassica rapa: Insight into the Glucosinolate Pathway

    PubMed Central

    Pino Del Carpio, Dunia; Basnet, Ram Kumar; Arends, Danny; Lin, Ke; De Vos, Ric C. H.; Muth, Dorota; Kodde, Jan; Boutilier, Kim; Bucher, Johan; Wang, Xiaowu; Jansen, Ritsert; Bonnema, Guusje

    2014-01-01

    Brassica rapa studies towards metabolic variation have largely been focused on the profiling of the diversity of metabolic compounds in specific crop types or regional varieties, but none aimed to identify genes with regulatory function in metabolite composition. Here we followed a genetical genomics approach to identify regulatory genes for six biosynthetic pathways of health-related phytochemicals, i.e carotenoids, tocopherols, folates, glucosinolates, flavonoids and phenylpropanoids. Leaves from six weeks-old plants of a Brassica rapa doubled haploid population, consisting of 92 genotypes, were profiled for their secondary metabolite composition, using both targeted and LC-MS-based untargeted metabolomics approaches. Furthermore, the same population was profiled for transcript variation using a microarray containing EST sequences mainly derived from three Brassica species: B. napus, B. rapa and B. oleracea. The biochemical pathway analysis was based on the network analyses of both metabolite QTLs (mQTLs) and transcript QTLs (eQTLs). Co-localization of mQTLs and eQTLs lead to the identification of candidate regulatory genes involved in the biosynthesis of carotenoids, tocopherols and glucosinolates. We subsequently focused on the well-characterized glucosinolate pathway and revealed two hotspots of co-localization of eQTLs with mQTLs in linkage groups A03 and A09. Our results indicate that such a large-scale genetical genomics approach combining transcriptomics and metabolomics data can provide new insights into the genetic regulation of metabolite composition of Brassica vegetables. PMID:25222144

  3. Methotrexate Is a JAK/STAT Pathway Inhibitor

    PubMed Central

    Thomas, Sally; Fisher, Katherine H.; Snowden, John A.; Danson, Sarah J.; Brown, Stephen; Zeidler, Martin P.

    2015-01-01

    Background The JAK/STAT pathway transduces signals from multiple cytokines and controls haematopoiesis, immunity and inflammation. In addition, pathological activation is seen in multiple malignancies including the myeloproliferative neoplasms (MPNs). Given this, drug development efforts have targeted the pathway with JAK inhibitors such as ruxolitinib. Although effective, high costs and side effects have limited its adoption. Thus, a need for effective low cost treatments remains. Methods & Findings We used the low-complexity Drosophila melanogaster pathway to screen for small molecules that modulate JAK/STAT signalling. This screen identified methotrexate and the closely related aminopterin as potent suppressors of STAT activation. We show that methotrexate suppresses human JAK/STAT signalling without affecting other phosphorylation-dependent pathways. Furthermore, methotrexate significantly reduces STAT5 phosphorylation in cells expressing JAK2 V617F, a mutation associated with most human MPNs. Methotrexate acts independently of dihydrofolate reductase (DHFR) and is comparable to the JAK1/2 inhibitor ruxolitinib. However, cells treated with methotrexate still retain their ability to respond to physiological levels of the ligand erythropoietin. Conclusions Aminopterin and methotrexate represent the first chemotherapy agents developed and act as competitive inhibitors of DHFR. Methotrexate is also widely used at low doses to treat inflammatory and immune-mediated conditions including rheumatoid arthritis. In this low-dose regime, folate supplements are given to mitigate side effects by bypassing the biochemical requirement for DHFR. Although independent of DHFR, the mechanism-of-action underlying the low-dose effects of methotrexate is unknown. Given that multiple pro-inflammatory cytokines signal through the pathway, we suggest that suppression of the JAK/STAT pathway is likely to be the principal anti-inflammatory and immunosuppressive mechanism-of-action of low-dose methotrexate. In addition, we suggest that patients with JAK/STAT-associated haematological malignancies may benefit from low-dose methotrexate treatments. While the JAK1/2 inhibitor ruxolitinib is effective, a £43,200 annual cost precludes widespread adoption. With an annual methotrexate cost of around £32, our findings represent an important development with significant future potential. PMID:26131691

  4. Cytochrome P450 Monooxygenases as Reporters for Circadian-Regulated Pathways1[C][W][OA

    PubMed Central

    Pan, Yinghong; Michael, Todd P.; Hudson, Matthew E.; Kay, Steve A.; Chory, Joanne; Schuler, Mary A.

    2009-01-01

    Cytochrome P450 monooxygenases (P450s) play important roles in the synthesis of diverse secondary compounds in Arabidopsis (Arabidopsis thaliana). Comparison of four data sets analyzing seedlings harvested over a 2-d period of constant conditions after growth with varying photoperiods and thermocycles recorded a total of 98 P450 loci as circadian regulated for at least one of the four conditions. Here, we further describe the circadian-regulated pathways using, as reporters, individual P450 loci that are likely to be rate limiting in secondary metabolic pathways. Reverse transcription-polymerase chain reaction gel blot analyses have confirmed circadian regulation of P450s in phenylpropanoid, carotenoid, oxylipin, glucosinolate, and brassinosteroid biosyntheses and have shown that both P450 and non-P450 genes in the many branches of the phenylpropanoid pathway have similar circadian patterns of expression. In silico analyses of the subsets of coregulated promoters have identified overrepresented promoter elements in various biosynthetic pathway genes, including MYB and MYB4 elements that are significantly more abundant in promoters for the core and lignin sections of phenylpropanoid metabolism. Interactions with these elements important for circadian regulation do not involve the MYB transcription factor PAP1, as previously proposed, since the expression patterns of circadian-regulated P450s are the same in pap1-D mutant seedlings as in wild-type seedlings. Further analysis of circadian-regulated promoters in other biochemical pathways provides us with the opportunity to identify novel promoter motifs that might be important in P450 circadian regulation. PMID:19386812

  5. Transcriptomic profiling of TK2 deficient human skeletal muscle suggests a role for the p53 signalling pathway and identifies growth and differentiation factor-15 as a potential novel biomarker for mitochondrial myopathies

    PubMed Central

    2014-01-01

    Background Mutations in the gene encoding thymidine kinase 2 (TK2) result in the myopathic form of mitochondrial DNA depletion syndrome which is a mitochondrial encephalomyopathy presenting in children. In order to unveil some of the mechanisms involved in this pathology and to identify potential biomarkers and therapeutic targets we have investigated the gene expression profile of human skeletal muscle deficient for TK2 using cDNA microarrays. Results We have analysed the whole transcriptome of skeletal muscle from patients with TK2 mutations and compared it to normal muscle and to muscle from patients with other mitochondrial myopathies. We have identified a set of over 700 genes which are differentially expressed in TK2 deficient muscle. Bioinformatics analysis reveals important changes in muscle metabolism, in particular, in glucose and glycogen utilisation, and activation of the starvation response which affects aminoacid and lipid metabolism. We have identified those transcriptional regulators which are likely to be responsible for the observed changes in gene expression. Conclusion Our data point towards the tumor suppressor p53 as the regulator at the centre of a network of genes which are responsible for a coordinated response to TK2 mutations which involves inflammation, activation of muscle cell death by apoptosis and induction of growth and differentiation factor 15 (GDF-15) in muscle and serum. We propose that GDF-15 may represent a potential novel biomarker for mitochondrial dysfunction although further studies are required. PMID:24484525

  6. The role of gene fusions in the evolution of metabolic pathways: the histidine biosynthesis case

    PubMed Central

    Fani, Renato; Brilli, Matteo; Fondi, Marco; Lió, Pietro

    2007-01-01

    Background Histidine biosynthesis is one of the best characterized anabolic pathways. There is a large body of genetic and biochemical information available, including operon structure, gene expression, and increasingly larger sequence databases. For over forty years this pathway has been the subject of extensive studies, mainly in Escherichia coli and Salmonella enterica, in both of which details of histidine biosynthesis appear to be identical. In these two enterobacteria the pathway is unbranched, includes a number of unusual reactions, and consists of nine intermediates; his genes are arranged in a compact operon (hisGDC [NB]HAF [IE]), with three of them (hisNB, hisD and hisIE) coding for bifunctional enzymes. We performed a detailed analysis of his gene fusions in available genomes to understand the role of gene fusions in shaping this pathway. Results The analysis of HisA structures revealed that several gene elongation events are at the root of this protein family: internal duplication have been identified by structural superposition of the modules composing the TIM-barrel protein. Several his gene fusions happened in distinct taxonomic lineages; hisNB originated within ?-proteobacteria and after its appearance it was transferred to Campylobacter species (?-proteobacteria) and to some Bacteria belonging to the CFB group. The transfer involved the entire his operon. The hisIE gene fusion was found in several taxonomic lineages and our results suggest that it probably happened several times in distinct lineages. Gene fusions involving hisIE and hisD genes (HIS4) and hisH and hisF genes (HIS7) took place in the Eukarya domain; the latter has been transferred to some ?-proteobacteria. Conclusion Gene duplication is the most widely known mechanism responsible for the origin and evolution of metabolic pathways; however, several other mechanisms might concur in the process of pathway assembly and gene fusion appeared to be one of the most important and common. PMID:17767732

  7. Jasmonate Signaling Pathway

    NSDL National Science Digital Library

    Robin Liechti (University of Lausanne; Gene Expression Laboratory and Faculty of Biology and Medicine REV)

    2006-02-14

    Jasmonates in plants are cyclic fatty acid–derived regulators structurally similar to prostaglandins in metazoans. These chemicals mediate many of plants' transcriptional responses to wounding and pathogenesis by acting as potent regulators for the expression of numerous frontline immune response genes, including those for defensins and antifungal proteins. Additionally, the pathway is critical for fertility. Ongoing genetic screens and protein-protein interaction assays are identifying components of the canonical jasmonate signaling pathway. A massive molecular machine, based on two multiprotein complexes, SCFCOI1 and the COP9 signalosome (CNS), plays a central role in jasmonate signaling. This machine functions in vivo as a ubiquitin ligase complex, probably targeting regulatory proteins, some of which are expected to be transcriptional repressors. Some defense-related mediators, notably salicylic acid, antagonize jasmonates in controlling the expression of many genes. In Arabidopsis, NONEXPRESSOR OF PR GENES (NPR1) mediates part of this interaction, with another layer of control provided further downstream by the mitogen-activated protein kinase (MAPK) homolog MPK4. Numerous other interpathway connections influence the jasmonate pathway. Insights from Arabidopsis have shown that an allele of the auxin signaling gene AXR1, for example, reduces the sensitivity of plants to jasmonate. APETALA2 (AP2)-domain transcription factors, such as ETHYLENE RESPONSE FACTOR 1 (ERF1), link the jasmonate pathway to the ethylene signaling pathway. As progress in characterizing several new mutants (some of which are hypersensitive to jasmonic acid) augments our understanding of jasmonate signaling, the Connections Map will be updated to include this new information.

  8. Noise decomposition of intracellular biochemical signaling networks using nonequivalent reporters

    PubMed Central

    Rhee, Alex; Cheong, Raymond; Levchenko, Andre

    2014-01-01

    Experimental measurements of biochemical noise have primarily focused on sources of noise at the gene expression level due to limitations of existing noise decomposition techniques. Here, we introduce a mathematical framework that extends classical extrinsic–intrinsic noise analysis and enables mapping of noise within upstream signaling networks free of such restrictions. The framework applies to systems for which the responses of interest are linearly correlated on average, although the framework can be easily generalized to the nonlinear case. Interestingly, despite the high degree of complexity and nonlinearity of most mammalian signaling networks, three distinct tumor necrosis factor (TNF) signaling network branches displayed linearly correlated responses, in both wild-type and perturbed versions of the network, across multiple orders of magnitude of ligand concentration. Using the noise mapping analysis, we find that the c-Jun N-terminal kinase (JNK) pathway generates higher noise than the NF-?B pathway, whereas the activation of c-Jun adds a greater amount of noise than the activation of ATF-2. In addition, we find that the A20 protein can suppress noise in the activation of ATF-2 by separately inhibiting the TNF receptor complex and JNK pathway through a negative feedback mechanism. These results, easily scalable to larger and more complex networks, pave the way toward assessing how noise propagates through cellular signaling pathways and create a foundation on which we can further investigate the relationship between signaling system architecture and biological noise. PMID:25404303

  9. Thermodynamic analysis of lignocellulosic biofuel production via a biochemical process: guiding technology selection and research focus.

    PubMed

    Sohel, M Imroz; Jack, Michael W

    2011-02-01

    The aim of this paper is to present an exergy analysis of bioethanol production process from lignocellulosic feedstock via a biochemical process to asses the overall thermodynamic efficiency and identify the main loss processes. The thermodynamic efficiency of the biochemical process was found to be 35% and the major inefficiencies of this process were identified as: the combustion of lignin for process heat and power production and the simultaneous scarification and co-fermentation process accounting for 67% and 27% of the lost exergy, respectively. These results were also compared with a previous analysis of a thermochemical process for producing biofuel. Despite fundamental differences, the biochemical and thermochemical processes considered here had similar levels of thermodynamic efficiency. Process heat and power production was the major contributor to exergy loss in both of the processes. Unlike the thermochemical process, the overall efficiency of the biochemical process largely depends on how the lignin is utilized. PMID:21036607

  10. A molecular structure matching approach to efficient identification of endogenous mammalian biochemical structures

    PubMed Central

    2015-01-01

    Metabolomics is the study of small molecules, called metabolites, of a cell, tissue or organism. It is of particular interest as endogenous metabolites represent the phenotype resulting from gene expression. A major challenge in metabolomics research is the structural identification of unknown biochemical compounds in complex biofluids. In this paper we present an efficient cheminformatics tool, BioSMXpress that uses known endogenous mammalian biochemicals and graph matching methods to identify endogenous mammalian biochemical structures in chemical structure space. The results of a comprehensive set of empirical experiments suggest that BioSMXpress identifies endogenous mammalian biochemical structures with high accuracy. BioSMXpress is 8 times faster than our previous work BioSM without compromising the accuracy of the predictions made. BioSMXpress is freely available at http://engr.uconn.edu/~rajasek/BioSMXpress.zip PMID:25859612

  11. Protein signaling via type III secretion pathways in phytopathogenic bacteria

    Microsoft Academic Search

    Mary Beth Mudgett; Brian J Staskawicz

    1998-01-01

    Progress in the genetic and biochemical dissection of the hrp-encoded type III secretion pathway has revealed new mechanisms by which phytophathogenic bacteria infect plants. The suggestion that bacterial gene products are ‘delivered to’ and ‘perceived by’ plants cells has fundamentally changed the way in which plant—bacterial interactions are now being viewed.

  12. Evidence for the shikimate pathway in apicomplexan parasites

    Microsoft Academic Search

    Fiona Roberts; Craig W. Roberts; Jennifer J. Johnson; Dennis E. Kyle; Tino Krell; John R. Coggins; Graham H. Coombs; Wilbur K. Milhous; Saul Tzipori; David J. P. Ferguson; Debopam Chakrabarti; Rima McLeod

    1998-01-01

    Parasites of the phylum Apicomplexa cause substantial morbidity, mortality and economic losses, and new medicines to treat them are needed urgently,. The shikimate pathway is an attractive target for herbicides and antimicrobial agents because it is essential in algae, higher plants, bacteria and fungi, but absent from mammals,. Here we present biochemical, genetic and chemotherapeutic evidence for the presence of

  13. Method for inverting reflection trace data from 3-D and 4-D seismic surveys and identifying subsurface fluid and pathways in and among hydrocarbon reservoirs based on impedance models

    DOEpatents

    He, Wei (New Milford, NJ); Anderson, Roger N. (New York, NY)

    1998-01-01

    A method is disclosed for inverting 3-D seismic reflection data obtained from seismic surveys to derive impedance models for a subsurface region, and for inversion of multiple 3-D seismic surveys (i.e., 4-D seismic surveys) of the same subsurface volume, separated in time to allow for dynamic fluid migration, such that small scale structure and regions of fluid and dynamic fluid flow within the subsurface volume being studied can be identified. The method allows for the mapping and quantification of available hydrocarbons within a reservoir and is thus useful for hydrocarbon prospecting and reservoir management. An iterative seismic inversion scheme constrained by actual well log data which uses a time/depth dependent seismic source function is employed to derive impedance models from 3-D and 4-D seismic datasets. The impedance values can be region grown to better isolate the low impedance hydrocarbon bearing regions. Impedance data derived from multiple 3-D seismic surveys of the same volume can be compared to identify regions of dynamic evolution and bypassed pay. Effective Oil Saturation or net oil thickness can also be derived from the impedance data and used for quantitative assessment of prospective drilling targets and reservoir management.

  14. Method for inverting reflection trace data from 3-D and 4-D seismic surveys and identifying subsurface fluid and pathways in and among hydrocarbon reservoirs based on impedance models

    DOEpatents

    He, W.; Anderson, R.N.

    1998-08-25

    A method is disclosed for inverting 3-D seismic reflection data obtained from seismic surveys to derive impedance models for a subsurface region, and for inversion of multiple 3-D seismic surveys (i.e., 4-D seismic surveys) of the same subsurface volume, separated in time to allow for dynamic fluid migration, such that small scale structure and regions of fluid and dynamic fluid flow within the subsurface volume being studied can be identified. The method allows for the mapping and quantification of available hydrocarbons within a reservoir and is thus useful for hydrocarbon prospecting and reservoir management. An iterative seismic inversion scheme constrained by actual well log data which uses a time/depth dependent seismic source function is employed to derive impedance models from 3-D and 4-D seismic datasets. The impedance values can be region grown to better isolate the low impedance hydrocarbon bearing regions. Impedance data derived from multiple 3-D seismic surveys of the same volume can be compared to identify regions of dynamic evolution and bypassed pay. Effective Oil Saturation or net oil thickness can also be derived from the impedance data and used for quantitative assessment of prospective drilling targets and reservoir management. 20 figs.

  15. Biochemical DSB-repair model for mammalian cells in G1 and early S phases of the cell cycle.

    PubMed

    Taleei, Reza; Nikjoo, Hooshang

    2013-08-30

    The paper presents a model of double strand breaks (DSB) repair in G1 and early S phases of the cell cycle. The model is based on a plethora of published information on biochemical modification of DSB induced by ionizing radiation. So far, three main DSB repair pathways have been identified, including nonhomologous end-joining (NHEJ), homologous recombination (HR), and microhomology-mediated end-joining (MMEJ). During G1 and early S phases of the cell cycle, NHEJ and MMEJ repair pathways are activated dependent on the type of double strand breaks. Simple DSB are a substrate for NHEJ, while complex DSB and DSB in heterochromatin require further end processing. Repair of all DSB start with NHEJ presynaptic processes, and depending on the type of DSB pursue simple ligation, further end processing prior to ligation, or resection. Using law of mass action the model is translated into a mathematical formalism. The solution of the formalism provides the step by step and overall repair kinetics. The overall repair kinetics are compared with the published experimental measurements. Our calculations are in agreement with the experimental results and show that the complex types of DSBs are repaired with slow repair kinetics. The G1 and early S phase model could be employed to predict the kinetics of DSB repair for damage induced by high LET radiation. PMID:23792210

  16. Genetic Interaction Analysis of TCF7L2 for Biochemical Recurrence after Radical Prostatectomy in Localized Prostate Cancer

    PubMed Central

    Chen, Chien-Shu; Huang, Chao-Yuan; Huang, Shu-Pin; Lin, Victor C.; Yu, Chia-Cheng; Chang, Ta-Yuan; Bao, Bo-Ying

    2015-01-01

    Backgroud: Accumulated evidence has demonstrated a significant role of the Wnt pathway in human prostate cancer. We hypothesize that genetic variants in the Wnt pathway effector, Transcription factor 7-like 2 (TCF7L2), may influence clinical outcomes in prostate cancer. Methods: We comprehensively selected 12 tagged single-nucleotide polymorphisms (SNPs) to capture majority of common variants across TCF7L2, and genotyped in 458 localized prostate cancer patients treated with radical prostatectomy (RP). Kaplan-Meier analysis, Cox proportional hazard model, and survival tree analyses were performed to identify significant SNPs that correlated with biochemical recurrence (BCR) after surgery. Results: A higher-order SNP-SNP interaction profile consisting of TCF7L2 rs7094463, rs10749127, and rs11196224 was significantly associated with BCR (Ptrend = 0.001). After adjusting for possible confounders, the genetic profile remained significant (Ptrend = 0.007). None of the studied SNPs were individually associated with BCR. Conclusions: Our results support a genetic interaction in the TCF7L2 SNPs as a predictor of disease recurrence after curative RP in localized prostate cancer patients. PMID:25678841

  17. Oncogenic Pathway Combinations Predict Clinical Prognosis in Gastric Cancer

    E-print Network

    Ooi, Chia Huey

    Many solid cancers are known to exhibit a high degree of heterogeneity in their deregulation of different oncogenic pathways. We sought to identify major oncogenic pathways in gastric cancer (GC) with significant relationships ...

  18. Sexually transmitted diseases putative drug target database: A comprehensive database of putative drug targets of pathogens identified by comparative genomics

    PubMed Central

    Malipatil, Vijayakumari; Madagi, Shivkumar; Bhattacharjee, Biplab

    2013-01-01

    Objective: Sexually transmitted diseases (STD) are the serious public health problems and also impose a financial burden on the economy. Sexually transmitted infections are cured with single or multiple antibiotics. However, in many cases the organism showed persistence even after treatment. In the current study, the set of druggable targets in STD pathogens have been identified by comparative genomics. Materials and Methods: The subtractive genomics scheme exploits the properties of non-homology, essentiality, membrane localization and metabolic pathway uniqueness in identifying the drug targets. To achieve the effective use of data and to understand properties of drug target under single canopy, an integrated knowledge database of drug targets in STD bacteria was created. Data for each drug targets include biochemical pathway, function, cellular localization, essentiality score and structural details. Results: The proteome of STD pathogens yielded 44 membrane associated proteins possessing unique metabolic pathways when subjected to the algorithm. The database can be accessed at http://biomedresearchasia.org/index.html. Conclusion: Diverse data merged in the common framework of this database is expected to be valuable not only for basic studies in clinical bioinformatics, but also for basic studies in immunological, biotechnological and clinical fields. PMID:24130375

  19. Stimulation, Monitoring, and Analysis of Pathway Dynamics by Metabolic Profiling in the Aromatic Amino Acid Pathway

    Microsoft Academic Search

    M. Oldiges; M. Kunze; D. Degenring; G. A. Sprenger; R. Takors

    2004-01-01

    Using a concerted approach of biochemical standard preparation, analytical access via LC-MS\\/MS, glucose pulse, metabolic profiling, and statistical data analysis, the metabolism dynamics in the aromatic amino acid pathway has been stimulated, monitored, and analyzed in different tyrosine-auxotrophic L-phenylalanine-producing Escherichia coli strains. During the observation window from -4 s (before) up to 27 s after the glucose pulse, the dynamics

  20. An unconventional pathway for reduction of CO2 to methane in CO-grown Methanosarcina acetivorans revealed by proteomics.

    PubMed

    Lessner, Daniel J; Li, Lingyun; Li, Qingbo; Rejtar, Tomas; Andreev, Victor P; Reichlen, Matthew; Hill, Kevin; Moran, James J; Karger, Barry L; Ferry, James G

    2006-11-21

    Methanosarcina acetivorans produces acetate, formate, and methane when cultured with CO as the growth substrate [Rother M, Metcalf WW (2004) Proc Natl Acad Sci USA 101:], which suggests novel features of CO metabolism. Here we present a genome-wide proteomic approach to identify and quantify proteins differentially abundant in response to growth on CO versus methanol or acetate. The results indicate that oxidation of CO to CO2 supplies electrons for reduction of CO2 to a methyl group by steps and enzymes of the pathway for CO2 reduction determined for other methane-producing species. However, proteomic and quantitative RT-PCR results suggest that reduction of the methyl group to methane involves novel methyltransferases and a coenzyme F420H2:heterodisulfide oxidoreductase system that generates a proton gradient for ATP synthesis not previously described for pathways reducing CO2 to methane. Biochemical assays support a role for the oxidoreductase, and transcriptional mapping identified an unusual operon structure encoding the oxidoreductase. The proteomic results further indicate that acetate is synthesized from the methyl group and CO by a reversal of initial steps in the pathway for conversion of acetate to methane that yields ATP by substrate level phosphorylation. The results indicate that M. acetivorans utilizes a pathway distinct from all known CO2 reduction pathways for methane formation that reflects an adaptation to the marine environment. Finally, the pathway supports the basis for a recently proposed primitive CO-dependent energy-conservation cycle that drove and directed the early evolution of life on Earth. PMID:17101988

  1. Design Principles of Biochemical Oscillators

    PubMed Central

    Novak, Béla; Tyson, John J.

    2009-01-01

    Cellular rhythms are generated by complex interactions among genes, proteins and metabolites. They are used to control every aspect of cell physiology from signaling, motility and development to growth, division and death. By considering specific examples of oscillatory processes, we pick out three general requirements for biochemical oscillations: delayed negative feedback, sufficient ‘nonlinearity’ of the reaction kinetics, and proper balancing of the time-scales of opposing chemical reactions. Positive feedback is one mechanism to delay the negative feedback signal. Biological oscillators can be classified according to the topology of the positive and negative feedback loops in the underlying regulatory mechanism. PMID:18971947

  2. Biochemical Validation of the Glyoxylate Cycle in the Cyanobacterium Chlorogloeopsis fritschii Strain PCC 9212.

    PubMed

    Zhang, Shuyi; Bryant, Donald A

    2015-05-29

    Cyanobacteria are important photoautotrophic bacteria with extensive but variable metabolic capacities. The existence of the glyoxylate cycle, a variant of the TCA cycle, is still poorly documented in cyanobacteria. Previous studies reported the activities of isocitrate lyase and malate synthase, the key enzymes of the glyoxylate cycle in some cyanobacteria, but other studies concluded that these enzymes are missing. In this study the genes encoding isocitrate lyase and malate synthase from Chlorogloeopsis fritschii PCC 9212 were identified, and the recombinant enzymes were biochemically characterized. Consistent with the presence of the enzymes of the glyoxylate cycle, C. fritschii could assimilate acetate under both light and dark growth conditions. Transcript abundances for isocitrate lyase and malate synthase increased, and C. fritschii grew faster, when the growth medium was supplemented with acetate. Adding acetate to the growth medium also increased the yield of poly-3-hydroxybutyrate. When the genes encoding isocitrate lyase and malate synthase were expressed in Synechococcus sp. PCC 7002, the acetate assimilation capacity of the resulting strain was greater than that of wild type. Database searches showed that the genes for the glyoxylate cycle exist in only a few other cyanobacteria, all of which are able to fix nitrogen. This study demonstrates that the glyoxylate cycle exists in a few cyanobacteria, and that this pathway plays an important role in the assimilation of acetate for growth in one of those organisms. The glyoxylate cycle might play a role in coordinating carbon and nitrogen metabolism under conditions of nitrogen fixation. PMID:25869135

  3. Mevalonate shunt pathway revisited

    SciTech Connect

    Watson, J.A.; Gonzalez-Pacanowska, D.; Havel, C.M.

    1987-05-01

    Full suppression of mammalian HMG-CoA reductase (HMGR) activity requires regulatory sterol and non-sterol products derived from mevalonate (MVA). The regulatory products identities are unknown. They have taken advantage of an established insect cell line (K/sub c/ cells) to identify the non-sterol isoprenoid regulatory signal (NSRS) molecule(s). Since K/sub c/ cells shunt minimally 40% of their MVA carbon, to non isoprenoid products, it is possible that the NSRS molecule(s) are also generated by this pathway. They report on investigations to elucidate the MVA shunt pathway. Intact K/sub c/ cells accumulate farnesol and geranylgeraniol with increasing exogenous MVA concentration. Supplemented K/sub c/ cells extracts rapidly convert (/sup 14/C) farnesol to ..cap alpha..,omega-dibasic prenoic acids (DCA) plus further degradation products. Two of the DCA products are 3,7-dimethyl 2,6-decadien 1,10-dioic acid and 3,7,11-trimethyl 2,6,10-dodecatrien 1,12-dioic acid. Similar acids are isolated from identical incubations with rat liver homogenates. Their results support MVA carbon being converted to non-isoprenoid products via polyprenols which in turn, are oxidatively catabolized, as DCAs, from the w-terminus. This metabolic capacity, exists in both mammalian and invertebrate cells and offers an alternative to shunt pathways proposed by other investigators.

  4. High-content screening identifies small molecules that remove nuclear foci, affect MBNL distribution and CELF1 protein levels via a PKC-independent pathway in myotonic dystrophy cell lines

    PubMed Central

    Ketley, Ami; Chen, Catherine Z.; Li, Xin; Arya, Sukrat; Robinson, Thelma E.; Granados-Riveron, Javier; Udosen, Inyang; Morris, Glenn E.; Holt, Ian; Furling, Denis; Chaouch, Soraya; Haworth, Ben; Southall, Noel; Shinn, Paul; Zheng, Wei; Austin, Christopher P.; Hayes, Christopher J.; Brook, J. David

    2014-01-01

    Myotonic dystrophy (DM) is a multi-system neuromuscular disorder for which there is no treatment. We have developed a medium throughput phenotypic assay, based on the identification of nuclear foci in DM patient cell lines using in situ hybridization and high-content imaging to screen for potentially useful therapeutic compounds. A series of further assays based on molecular features of DM have also been employed. Two compounds that reduce and/or remove nuclear foci have been identified, Ro 31-8220 and chromomycin A3. Ro 31-8220 is a PKC inhibitor, previously shown to affect the hyperphosphorylation of CELF1 and ameliorate the cardiac phenotype in a DM1 mouse model. We show that the same compound eliminates nuclear foci, reduces MBNL1 protein in the nucleus, affects ATP2A1 alternative splicing and reduces steady-state levels of CELF1 protein. We demonstrate that this effect is independent of PKC activity and conclude that this compound may be acting on alternative kinase targets within DM pathophysiology. Understanding the activity profile for this compound is key for the development of targeted therapeutics in the treatment of DM. PMID:24179176

  5. Physiological, biochemical and transcriptional analysis of onion bulbs during storage

    PubMed Central

    Chope, Gemma A.; Cools, Katherine; Hammond, John P.; Thompson, Andrew J.; Terry, Leon A.

    2012-01-01

    Background and Aims During the transition from endo-dormancy to eco-dormancy and subsequent growth, the onion bulb undergoes the transition from sink organ to source, to sustain cell division in the meristematic tissue. The mechanisms controlling these processes are not fully understood. Here, a detailed analysis of whole onion bulb physiological, biochemical and transcriptional changes in response to sprouting is reported, enabling a better knowledge of the mechanisms regulating post-harvest onion sprout development. Methods Biochemical and physiological analyses were conducted on different cultivars (‘Wellington’, ‘Sherpa’ and ‘Red Baron’) grown at different sites over 3 years, cured at different temperatures (20, 24 and 28 °C) and stored under different regimes (1, 3, 6 and 6 ? 1 °C). In addition, the first onion oligonucleotide microarray was developed to determine differential gene expression in onion during curing and storage, so that transcriptional changes could support biochemical and physiological analyses. Key Results There were greater transcriptional differences between samples at harvest and before sprouting than between the samples taken before and after sprouting, with some significant changes occurring during the relatively short curing period. These changes are likely to represent the transition from endo-dormancy to sprout suppression, and suggest that endo-dormancy is a relatively short period ending just after curing. Principal component analysis of biochemical and physiological data identified the ratio of monosaccharides (fructose and glucose) to disaccharide (sucrose), along with the concentration of zeatin riboside, as important factors in discriminating between sprouting and pre-sprouting bulbs. Conclusions These detailed analyses provide novel insights into key regulatory triggers for sprout dormancy release in onion bulbs and provide the potential for the development of biochemical or transcriptional markers for sprout initiation. Evidence presented herein also suggests there is no detrimental effect on bulb storage life and quality caused by curing at 20 °C, producing a considerable saving in energy and costs. PMID:22234560

  6. Biochemical abnormalities in Pearson syndrome.

    PubMed

    Crippa, Beatrice Letizia; Leon, Eyby; Calhoun, Amy; Lowichik, Amy; Pasquali, Marzia; Longo, Nicola

    2015-03-01

    Pearson marrow-pancreas syndrome is a multisystem mitochondrial disorder characterized by bone marrow failure and pancreatic insufficiency. Children who survive the severe bone marrow dysfunction in childhood develop Kearns-Sayre syndrome later in life. Here we report on four new cases with this condition and define their biochemical abnormalities. Three out of four patients presented with failure to thrive, with most of them having normal development and head size. All patients had evidence of bone marrow involvement that spontaneously improved in three out of four patients. Unique findings in our patients were acute pancreatitis (one out of four), renal Fanconi syndrome (present in all patients, but symptomatic only in one), and an unusual organic aciduria with 3-hydroxyisobutyric aciduria in one patient. Biochemical analysis indicated low levels of plasma citrulline and arginine, despite low-normal ammonia levels. Regression analysis indicated a significant correlation between each intermediate of the urea cycle and the next, except between ornithine and citrulline. This suggested that the reaction catalyzed by ornithine transcarbamylase (that converts ornithine to citrulline) might not be very efficient in patients with Pearson syndrome. In view of low-normal ammonia levels, we hypothesize that ammonia and carbamylphosphate could be diverted from the urea cycle to the synthesis of nucleotides in patients with Pearson syndrome and possibly other mitochondrial disorders. PMID:25691415

  7. Pathway Databases: A Case Study in Computational Symbolic Theories

    NSDL National Science Digital Library

    Peter Karp (SRI International; Bioinformatics Research Group)

    2001-09-14

    A pathway database (DB) is a DB that describes biochemical pathways, reactions, and enzymes. The EcoCyc pathway DB (see http://ecocyc.org) describes the metabolic, transport, and genetic-regulatory networks of Escherichia coli. EcoCyc is an example of a computational symbolic theory, which is a DB that structures a scientific theory within a formal ontology so that it is available for computational analysis. It is argued that by encoding scientific theories in symbolic form, we open new realms of analysis and understanding for theories that would otherwise be too large and complex for scientists to reason with effectively.

  8. The HEART Pathway Randomized Trial

    PubMed Central

    Mahler, Simon A.; Riley, Robert F.; Hiestand, Brian C.; Russell, Gregory B.; Hoekstra, James W.; Lefebvre, Cedric W.; Nicks, Bret A.; Cline, David M.; Askew, Kim L.; Elliott, Stephanie B.; Herrington, David M.; Burke, Gregory L.; Miller, Chadwick D.

    2015-01-01

    Background The HEART Pathway is a decision aid designed to identify emergency department patients with acute chest pain for early discharge. No randomized trials have compared the HEART Pathway with usual care. Methods and Results Adult emergency department patients with symptoms related to acute coronary syndrome without ST-elevation on ECG (n=282) were randomized to the HEART Pathway or usual care. In the HEART Pathway arm, emergency department providers used the HEART score, a validated decision aid, and troponin measures at 0 and 3 hours to identify patients for early discharge. Usual care was based on American College of Cardiology/American Heart Association guidelines. The primary outcome, objective cardiac testing (stress testing or angiography), and secondary outcomes, index length of stay, early discharge, and major adverse cardiac events (death, myocardial infarction, or coronary revascularization), were assessed at 30 days by phone interview and record review. Participants had a mean age of 53 years, 16% had previous myocardial infarction, and 6% (95% confidence interval, 3.6%–9.5%) had major adverse cardiac events within 30 days of randomization. Compared with usual care, use of the HEART Pathway decreased objective cardiac testing at 30 days by 12.1% (68.8% versus 56.7%; P=0.048) and length of stay by 12 hours (9.9 versus 21.9 hours; P=0.013) and increased early discharges by 21.3% (39.7% versus 18.4%; P<0.001). No patients identified for early discharge had major adverse cardiac events within 30 days. Conclusions The HEART Pathway reduces objective cardiac testing during 30 days, shortens length of stay, and increases early discharges. These important efficiency gains occurred without any patients identified for early discharge suffering MACE at 30 days. PMID:25737484

  9. Oxidative biodegradation pathways of PAHs

    SciTech Connect

    Cerniglia, C.E. [National Center for Toxicological Research, Jefferson, AR (United States)

    1993-12-31

    Polycyclic aromatic hydrocarbons (PAHs) constitute a class of hazardous organic chemical consisting of three of more fused benzene rings in linear, angular and cluster arrangements. PAHs mostly occur as a result of fossil fuel combustion, as by-product of industrial processing and during the cooking of foods. A catabolically diverse microbial community, consisting of bacteria, fungi and algae, metabolizes aromatic compounds. Molecular oxygen is essential for the initial hydroxylation of polycyclic aromatic hydrocarbons by microorganisms. In contrast to bacteria, filamentous fungi use hydroxylation as a prelude to detoxification rather than to catabolism and assimilation. The biochemical principles underlying the degradation of polycyclic aromatic hydrocarbons will be discussed. The oxidative pathways of polycyclic aromatic hydrocarbon catabolism will be discussed. Studies will be presented on the relationship between the chemical structure of the polycyclic aromatic hydrocarbon and the rate of polycyclic aromatic hydrocarbon biodegradation in aquatic and terrestrial ecosystems.

  10. Discovery and Reconstitution of the Cycloclavine Biosynthetic Pathway—Enzymatic Formation of a Cyclopropyl Group**

    PubMed Central

    Jakubczyk, Dorota; Caputi, Lorenzo; Hatsch, Anaëlle; Nielsen, Curt A F; Diefenbacher, Melanie; Klein, Jens; Molt, Andrea; Schröder, Hartwig; Cheng, Johnathan Z; Naesby, Michael; O'Connor, Sarah E

    2015-01-01

    The ergot alkaloids, a class of fungal-derived natural products with important biological activities, are derived from a common intermediate, chanoclavine-I, which is elaborated into a set of diverse structures. Herein we report the discovery of the biosynthetic pathway of cycloclavine, a complex ergot alkaloid containing a cyclopropyl moiety. We used a yeast-based expression platform along with in?vitro biochemical experiments to identify the enzyme that catalyzes a rearrangement of the chanoclavine-I intermediate to form a cyclopropyl moiety. The resulting compound, cycloclavine, was produced in yeast at titers of >500?mg?L?1, thus demonstrating the feasibility of the heterologous expression of these complex alkaloids. PMID:25712404

  11. Genomic pathways database and biological data management.

    PubMed

    Ozsoyoglu, Z M; Ozsoyoglu, G; Nadeau, J

    2006-08-01

    In this paper, we discuss the properties of biological data and challenges it poses for data management, and argue that, in order to meet the data management requirements for 'digital biology', careful integration of the existing technologies and the development of new data management techniques for biological data are needed. Based on this premise, we present PathCase: Case Pathways Database System. PathCase is an integrated set of software tools for modelling, storing, analysing, visualizing and querying biological pathways data at different levels of genetic, molecular, biochemical and organismal detail. The novel features of the system include: (i) genomic information integrated with other biological data and presented starting from pathways; (ii) design for biologists who are possibly unfamiliar with genomics, but whose research is essential for annotating gene and genome sequences with biological functions; (iii) database design, implementation and graphical tools which enable users to visualize pathways data in multiple abstraction levels and to pose exploratory queries; (iv) a wide range of different types of queries including, 'path' and 'neighbourhood queries' and graphical visualization of query outputs; and (v) an implementation that allows for web (XML)-based dissemination of query outputs (i.e. pathways data in BIOPAX format) to researchers in the community, giving them control on the use of pathways data. PMID:16887001

  12. Steady state analysis of metabolic pathways using Petri nets.

    PubMed

    Voss, Klaus; Heiner, Monika; Koch, Ina

    2003-01-01

    Computer assisted analysis and simulation of biochemical pathways can improve the understanding of the structure and the dynamics of cell processes considerably. The construction and quantitative analysis of kinetic models is often impeded by the lack of reliable data. However, as the topological structure of biochemical systems can be regarded to remain constant in time, a qualitative analysis of a pathway model was shown to be quite promising as it can render a lot of useful knowledge, e. g., about its structural invariants. The topic of this paper are pathways whose substances have reached a dynamic concentration equilibrium (steady state). It is argued that appreciated tools from biochemistry and also low-level Petri nets can yield only part of the desired results, whereas executable high-level net models lead to a number of valuable additional insights by combining symbolic analysis and simulation. PMID:14700469

  13. Survival and apoptotic pathways initiated by TNF-alpha: modeling and predictions.

    PubMed

    Rangamani, Padmini; Sirovich, Lawrence

    2007-08-01

    We present a mathematical model which includes TNF-alpha initiated survival and apoptotic cascades, as well as nuclear transcription of IkappaB. These pathways play a crucial role in deciding cell fate in response to inflammation and infection. Our model incorporates known specific protein-protein interactions as identified by experiments. Using these biochemical interactions, we develop a mathematical model of the NF-kappaB-mediated survival and caspase-mediated apoptosis pathways. Using mass action kinetics, we follow the formation of the survival and late complexes as well as the dynamics of DNA fragmentation. The effect of TNF-alpha concentration on DNA fragmentation is modeled and compares well with experiment. Nuclear transcription is also modeled phenomenologically by means of time lagged cytosolic concentrations. This results in transcription related concentrations undergoing under-damped oscillations, in qualitative and quantitative agreement with experiment. Using a tumor cell as a hypothetical model, we explore the interplay between the components of the survival and apoptotic pathways. Results are presented which make predictions on the limits of cellular oscillations in terms of time delay, initial concentration ratios and other features of the model. The model also makes clear predictions on cell viability in terms of DNA damage within the framework of TNF-alpha stimulus duration. PMID:17171720

  14. Growth hormone activity in mitochondria depends on GH receptor Box 1 and involves caveolar pathway targeting

    SciTech Connect

    Perret-Vivancos, Cecile [CNRS UMR 5123, Bat. R. Dubois, Universite Claude Bernard-Lyon 1, 43 Bd du 11 Novembre 1918, 69622 Villeurbanne cedex (France); Abbate, Aude [CNRS UMR 5123, Bat. R. Dubois, Universite Claude Bernard-Lyon 1, 43 Bd du 11 Novembre 1918, 69622 Villeurbanne cedex (France); Ardail, Dominique [INSERM U189-Faculte de medecine Lyon Sud, 69921 Oullins cedex (France); Raccurt, Mireille [CNRS UMR 5123, Bat. R. Dubois, Universite Claude Bernard-Lyon 1, 43 Bd du 11 Novembre 1918, 69622 Villeurbanne cedex (France); Usson, Yves [UMR 5525 CNRS, Institut de l'Ingenierie de l'Information de Sante (IN3S) Domaine de la Merci, Universite Joseph Fourier, 38706 La Tronche cedex (France); Lobie, Peter E. [Liggins Institute, University of Aukland, 2-6 Park Avenue, Private Bag, Aukland 92019 (New Zealand); Morel, Gerard [CNRS UMR 5123, Bat. R. Dubois, Universite Claude Bernard-Lyon 1, 43 Bd du 11 Novembre 1918, 69622 Villeurbanne cedex (France)]. E-mail: gerard.morel@univ-lyon1.fr

    2006-02-01

    Growth hormone (GH) binding to its receptor (GHR) initiates GH-dependent signal transduction and internalization pathways to generate the biological effects. The precise role and way of action of GH on mitochondrial function are not yet fully understood. We show here that GH can stimulate cellular oxygen consumption in CHO cells transfected with cDNA coding for the full-length GHR. By using different GHR cDNA constructs, we succeeded in determining the different parts of the GHR implicated in the mitochondrial response to GH. Polarography and two-photon excitation fluorescence microscopy analysis showed that the Box 1 of the GHR intracellular domain was required for an activation of the mitochondrial respiration in response to a GH exposure. However, confocal laser scanning microscopy demonstrated that cells lacking the GHR Box 1 could efficiently internalize the hormone. We demonstrated that internalization mediated either by clathrin-coated pits or by caveolae was able to regulate GH mitochondrial effect: these two pathways are both essential to obtain the GH stimulatory action on mitochondrial function. Moreover, electron microscopic and biochemical approaches allowed us to identify the caveolar pathway as essential for targeting GH and GHR to mitochondria.

  15. A point mutation in ftmD blocks the fumitremorgin biosynthetic pathway in Aspergillus fumigatus strain Af293.

    PubMed

    Kato, Naoki; Suzuki, Hirokazu; Okumura, Hideo; Takahashi, Shunji; Osada, Hiroyuki

    2013-01-01

    Fumitremorgins (FTMs), tremorgenic mycotoxins produced by the human pathogen Aspergillus fumigatus, are prenylated indole alkaloids that have been extensively studied in view of their diverse chemical structures and biological activities. Their biosynthetic gene (ftm) cluster was identified on the basis of the genome sequence of A. fumigatus. However, it has been reported that the ftm cluster in genome reference strain Af293 is inactive, which makes complete understanding of the FTM pathway difficult. Hence, we used an FTM-producing strain of A. fumigatus, BM939, to dissect the FTM pathway. Here, we delineate the genetic determinant for the observed defect in the FTM pathway in A. fumigatus Af293. Metabolite profiling and sequence comparison of the two strains revealed a point mutation in ftmD as a possible cause of altered metabolite production in strain Af293. FTM production in Af293 was restored when a DNA fragment containing ftmD from BM939 was introduced. Biochemical analysis indicated that FtmD is a methyltransferase that catalyzes the conversion of 6-hydroxytryprostatin B into tryprostatin A. The mutated FtmD retained enzymatic activity but did not function under physiological conditions, resulting in blockage of the FTM pathway in A. fumigatus Af293. PMID:23649274

  16. Pathway-based Biomarkers for Breast Cancer in Proteomics.

    PubMed

    Zhang, Fan; Deng, Youping; Wang, Mu; Cui, Li; Drabier, Renee

    2014-01-01

    Genes do not function alone but through complex biological pathways. Pathway-based biomarkers may be a reliable diagnostic tool for early detection of breast cancer due to the fact that breast cancer is not a single homogeneous disease. We applied Integrated Pathway Analysis Database (IPAD) and Gene Set Enrichment Analysis (GSEA) approaches to the study of pathway-based biomarker discovery problem in breast cancer proteomics. Our strategy for identifying and analyzing pathway-based biomarkers are threefold. Firstly, we performed pathway analysis with IPAD to build the gene set database. Secondly, we ran GSEA to identify 16 pathway-based biomarkers. Lastly, we built a Support Vector Machine model with three-way data split and fivefold cross-validation to validate the biomarkers. The approach-unraveling the intricate pathways, networks, and functional contexts in which genes or proteins function-is essential to the understanding molecular mechanisms of pathway-based biomarkers in breast cancer. PMID:25972728

  17. SLOPPINESS, MODELING, AND EVOLUTION IN BIOCHEMICAL NETWORKS

    E-print Network

    Sethna, James P.

    SLOPPINESS, MODELING, AND EVOLUTION IN BIOCHEMICAL NETWORKS A Dissertation Presented to the Faculty #12;SLOPPINESS, MODELING, AND EVOLUTION IN BIOCHEMICAL NETWORKS Ryan Nicholas Gutenkunst, Ph of such models to parameter changes are generically `sloppy', with eigenvalues roughly evenly spaced over many

  18. Biochemical transformation of solid carbonaceous material

    DOEpatents

    Lin, Mow S. (Rocky Point, NY); Premuzic, Eugene T. (East Moriches, NY)

    2001-09-25

    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.

  19. Diagnosis of hyperandrogenism: biochemical criteria.

    PubMed

    Stanczyk, Frank Z

    2006-06-01

    Biochemical derangements in ovarian, adrenal, and peripheral androgen production and metabolism play an important role in underlying causes of hyperandrogenism. Specific diagnostic serum markers such as testosterone (total) and dehydroepiandrosterone sulfate (DHEAS), respectively, may be helpful in the diagnosis of ovarian and adrenal hyperandrogenism, respectively. Validated immunoassays or mass spectrometry assays should be used to quantify testosterone, DHEAS and other principal androgens. Free testosterone measurements, determined by equilibrium dialysis or the calculated method, are advocated for routine evaluation of more subtle forms of hyperandrogenism. The skin, with its pilosebaceous units (PSUs), is an important site of active androgen production. A key regulator in PSUs is 5alpha-reductase, which transforms testosterone or androstenedione to dihydrotestosterone (DHT). DHT in blood is not effective in indicating the presence of hyperandrogenism. However, distal metabolites of DHT have been shown to be good markers of clinical manifestations of hirsutism, acne and alopecia. Assays for these peripheral markers need improvement for routine clinical testing. PMID:16772150

  20. De novo pyrimidine nucleotide synthesis mainly occurs outside of plastids, but a previously undiscovered nucleobase importer provides substrates for the essential salvage pathway in Arabidopsis.

    PubMed

    Witz, Sandra; Jung, Benjamin; Fürst, Sarah; Möhlmann, Torsten

    2012-04-01

    Nucleotide de novo synthesis is highly conserved among organisms and represents an essential biochemical pathway. In plants, the two initial enzymatic reactions of de novo pyrimidine synthesis occur in the plastids. By use of green fluorescent protein fusions, clear support is provided for a localization of the remaining reactions in the cytosol and mitochondria. This implies that carbamoyl aspartate, an intermediate of this pathway, must be exported and precursors of pyrimidine salvage (i.e., nucleobases or nucleosides) are imported into plastids. A corresponding uracil transport activity could be measured in intact plastids isolated from cauliflower (Brassica oleracea) buds. PLUTO (for plastidic nucleobase transporter) was identified as a member of the Nucleobase:Cation-Symporter1 protein family from Arabidopsis thaliana, capable of transporting purine and pyrimidine nucleobases. A PLUTO green fluorescent protein fusion was shown to reside in the plastid envelope after expression in Arabidopsis protoplasts. Heterologous expression of PLUTO in an Escherichia coli mutant lacking the bacterial uracil permease uraA allowed a detailed biochemical characterization. PLUTO transports uracil, adenine, and guanine with apparent affinities of 16.4, 0.4, and 6.3 ?M, respectively. Transport was markedly inhibited by low concentrations of a proton uncoupler, indicating that PLUTO functions as a proton-substrate symporter. Thus, a protein for the absolutely required import of pyrimidine nucleobases into plastids was identified. PMID:22474184

  1. (R)-Cysteate-nitrogen assimilation by Cupriavidus necator H16 with excretion of 3-sulfolactate: a patchwork pathway.

    PubMed

    Mayer, Jutta; Denger, Karin; Hollemeyer, Klaus; Schleheck, David; Cook, Alasdair M

    2012-11-01

    Cupriavidus necator H16 grew exponentially with (R)-cysteate, a structural analogue of aspartate, as sole source of nitrogen in succinate-salts medium. Utilization of cysteate was quantitative and concomitant with growth and with the excretion of the deaminated product (R)-sulfolactate, which was identified thoroughly. The deaminative pathway started with transport of (R)-cysteate into the cell, which we attributed to an aspartate transporter. Transamination to sulfopyruvate involved an aspartate/(R)-cysteate:2-oxoglutarate aminotransferase (Aoa/Coa) and regeneration of the amino group acceptor by NADP?-coupled glutamate dehydrogenase. Reduction of sulfopyruvate to (R)-sulfolactate was catalyzed by a (S)-malate/(R)-sulfolactate dehydrogenase (Mdh/Sdh). Excretion of the sulfolactate could be attributed to the sulfite/organosulfonate exporter TauE, which was co-encoded and co-expressed, with sulfoacetaldehyde acetyltransferase (Xsc), though Xsc was irrelevant to the current pathway. The metabolic enzymes could be assayed biochemically. Aoa/Coa and Mdh/Sdh were highly enriched by protein separation, partly characterized, and the relevant locus-tags identified by peptide-mass fingerprinting. Finally, RT-PCR was used to confirm the transcription of all appropriate genes. We thus demonstrated that Cupriavidus necator H16 uses a patchwork pathway by recruitment of 'housekeeping' genes and sulfoacetaldehyde-degradative genes to scavenge for (R)-cysteate-nitrogen. PMID:22797525

  2. Chemical and Biochemical Engineering Getting Computing Help at Chemical and

    E-print Network

    Chemical and Biochemical Engineering Getting Computing Help at Chemical and Biochemical Engineering Help for Departmental Systems. Users of computing systems at Chemical and Biochemical Engineering can get technical support for most issues by contacting the Systems Administrator at help

  3. Metabolic Signature of Sun Exposed Skin Suggests Catabolic Pathway Overweighs Anabolic Pathway

    PubMed Central

    Randhawa, Manpreet; Sangar, Vineet; Tucker-Samaras, Samantha; Southall, Michael

    2014-01-01

    Skin chronically exposed to sun results in phenotypic changes referred as photoaging. This aspect of aging has been studied extensively through genomic and proteomic tools. Metabolites, the end product are generated as a result of biochemical reactions are often studied as a culmination of complex interplay of gene and protein expression. In this study, we focused exclusively on the metabolome to study effects from sun-exposed and sun-protected skin sites from 25 human subjects. We generated a highly accurate metabolomic signature for the skin that is exposed to sun. Biochemical pathway analysis from this data set showed that sun-exposed skin resides under high oxidative stress and the chains of reactions to produce these metabolites are inclined toward catabolism rather than anabolism. These catabolic activities persuade the skin cells to generate metabolites through the salvage pathway instead of de novo synthesis pathways. Metabolomic profile suggests catabolic pathways and reactive oxygen species operate in a feed forward fashion to alter the biology of sun exposed skin. PMID:24603693

  4. Escherichia coli redox mutants as microbial cell factories for the synthesis of reduced biochemicals

    PubMed Central

    Ruiz, Jimena A.; de Almeida, Alejandra; Godoy, Manuel S.; Mezzina, Mariela P.; Bidart, Gonzalo N.; Méndez, Beatriz S.; Pettinari, M. Julia; Nikel, Pablo I.

    2013-01-01

    Bioprocesses conducted under conditions with restricted O2 supply are increasingly exploited for the synthesis of reduced biochemicals using different biocatalysts. The model facultative aerobe Escherichia coli, the microbial cell factory par excellence, has elaborate sensing and signal transduction mechanisms that respond to the availability of electron acceptors and alternative carbon sources in the surrounding environment. In particular, the ArcBA and CreBC two-component signal transduction systems are largely responsible for the metabolic regulation of redox control in response to O2 availability and carbon source utilization, respectively. Significant advances in the understanding of the biochemical, genetic, and physiological duties of these regulatory systems have been achieved in recent years. This situation allowed to rationally-design novel engineering approaches that ensure optimal carbon and energy flows within central metabolism, as well as to manipulate redox homeostasis, in order to optimize the production of industrially-relevant metabolites. In particular, metabolic flux analysis provided new clues to understand the metabolic regulation mediated by the ArcBA and CreBC systems. Genetic manipulation of these regulators proved useful for designing microbial cells factories tailored for the synthesis of reduced biochemicals with added value, such as poly(3-hydroxybutyrate), under conditions with restricted O2 supply. This network-wide strategy is in contrast with traditional metabolic engineering approaches, that entail direct modification of the pathway(s) at stake, and opens new avenues for the targeted modulation of central catabolic pathways at the transcriptional level. PMID:24688679

  5. Pathways for virus assembly around nucleic acids

    E-print Network

    Perlmutter, Jason D; Hagan, Michael F

    2014-01-01

    Understanding the pathways by which viral capsid proteins assemble around their genomes could identify key intermediates as potential drug targets. In this work we use computer simulations to characterize assembly over a wide range of capsid protein-protein interaction strengths and solution ionic strengths. We find that assembly pathways can be categorized into two classes, in which intermediates are either predominantly ordered or disordered. Our results suggest that estimating the protein-protein and the protein-genome binding affinities may be sufficient to predict which pathway occurs. Furthermore, the calculated phase diagrams suggest that knowledge of the dominant assembly pathway and its relationship to control parameters could identify optimal strategies to thwart or redirect assembly to block infection. Finally, analysis of simulation trajectories suggests that the two classes of assembly pathways can be distinguished in single molecule fluorescence correlation spectroscopy or bulk time resolved sma...

  6. Pathways for virus assembly around nucleic acids

    E-print Network

    Jason D Perlmutter; Matthew R Perkett; Michael F Hagan

    2014-05-13

    Understanding the pathways by which viral capsid proteins assemble around their genomes could identify key intermediates as potential drug targets. In this work we use computer simulations to characterize assembly over a wide range of capsid protein-protein interaction strengths and solution ionic strengths. We find that assembly pathways can be categorized into two classes, in which intermediates are either predominantly ordered or disordered. Our results suggest that estimating the protein-protein and the protein-genome binding affinities may be sufficient to predict which pathway occurs. Furthermore, the calculated phase diagrams suggest that knowledge of the dominant assembly pathway and its relationship to control parameters could identify optimal strategies to thwart or redirect assembly to block infection. Finally, analysis of simulation trajectories suggests that the two classes of assembly pathways can be distinguished in single molecule fluorescence correlation spectroscopy or bulk time resolved small angle x-ray scattering experiments.

  7. UDP-galactose 4’-epimerase from the liver fluke, Fasciola hepatica: biochemical characterisation of the enzyme and identification of inhibitors

    PubMed Central

    Zinsser, Veronika L.; Lindert, Steffen; Banford, Samantha; Hoey, Elizabeth M.; Trudgett, Alan; Timson, David J.

    2015-01-01

    The Leloir pathway enzyme UDP-galactose 4’-epimerase from the common liver fluke Fasciola hepatica (FhGALE) was identified and characterised. The enzyme can be expressed in, and purified from, Escherichia coli. The recombinant enzyme is active: the Km (470 µM) is higher than the corresponding human enzyme (HsGALE), whereas the kcat (2.3 s?1) is substantially lower. FhGALE binds NAD+ and was shown to be dimeric by analytical gel filtration. Like the human and yeast GALEs, FhGALE is stabilised by the substrate UDP-galactose. Molecular modelling predicted that FhGALE adopts a similar overall fold to HsGALE and that tyrosine 155 is likely to be the catalytically critical residue in the active site. In silico screening of the NCI DTP library identified 40 potential inhibitors of FhGALE which were tested in vitro. Of these, six showed concentration-dependent inhibition of FhGALE, some with nanomolar IC50 values. Two inhibitors (5-fluoroorotate and N-[(benzyloxy)carbonyl]leucyltryptophan) demonstrated selectivity for FhGALE over HsGALE. These compounds also thermally destabilised FhGALE in a concentration-dependent manner. Interestingly the selectivity of 5-fluoroorotate was not shown by orotic acid, which differs in structure by one fluorine atom. These results demonstrate that, despite the structural and biochemical similarities of FhGALE and HsGALE, it is possible to discover compounds which preferentially inhibit FhGALE. PMID:25124392

  8. Premetazoan origin of the hippo signaling pathway.

    PubMed

    Sebé-Pedrós, Arnau; Zheng, Yonggang; Ruiz-Trillo, Iñaki; Pan, Duojia

    2012-01-26

    Nonaggregative multicellularity requires strict control of cell number. The Hippo signaling pathway coordinates cell proliferation and apoptosis and is a central regulator of organ size in animals. Recent studies have shown the presence of key members of the Hippo pathway in nonbilaterian animals, but failed to identify this pathway outside Metazoa. Through comparative analyses of recently sequenced holozoan genomes, we show that Hippo pathway components, such as the kinases Hippo and Warts, the coactivator Yorkie, and the transcription factor Scalloped, were already present in the unicellular ancestors of animals. Remarkably, functional analysis of Hippo components of the amoeboid holozoan Capsaspora owczarzaki, performed in Drosophila melanogaster, demonstrate that the growth-regulatory activity of the Hippo pathway is conserved in this unicellular lineage. Our findings show that the Hippo pathway evolved well before the origin of Metazoa and highlight the importance of Hippo signaling as a key developmental mechanism predating the origin of Metazoa. PMID:22832104

  9. The anhydrofructose pathway of glycogen catabolism.

    PubMed

    Yu, Shukun

    2008-12-01

    In many living forms, glucose is stored in the polymeric form of glycogen and starch as a source of carbon and energy. Upon need, these polymers are broken down to their building block glucose in the presence of water and hydrolases, and glucose 1-phosphate in the presence of phosphate and phosphorylase. In the last decade, we established an alternative glycogen catabolic pathway, the so-called Anhydrofructose (AF) pathway, the description of which was approved by IUBMB in 2006. It is a pathway on the formation of an array of secondary metabolites from glycogen via the central intermediate 1,5-anhydro-D-fructose (AF). Furthermore, we demonstrated the occurrence of this pathway in both eukaryota and prokaryota. Metabolites of this pathway have been identified in mammals including humans. In this review, the physiological and molecular functions of these metabolites in the AF pathway as well as its regulation are discussed. PMID:18785261

  10. Genome-Wide Expression Analysis Reveals Diverse Effects of Acute Nicotine Exposure on Neuronal Function-Related Genes and Pathways

    PubMed Central

    Wang, Ju; Cui, Wenyan; Wei, Jinxue; Sun, Dongxiao; Gutala, Ramana; Gu, Jun; Li, Ming D.

    2011-01-01

    Previous human and animal studies demonstrate that acute nicotine exposure has complicated influences on the function of the nervous system, which may lead to long-lasting effects on the behavior and physiology of the subject. To determine the genes and pathways that might account for long-term changes after acute nicotine exposure, a pathway-focused oligoarray specifically designed for drug addiction research was used to assess acute nicotine effect on gene expression in the neuron-like SH-SY5Y cells. Our results showed that 295 genes involved in various biological functions were differentially regulated by 1?h of nicotine treatment. Among these genes, the expression changes of 221 were blocked by mecamylamine, indicating that the majority of nicotine-modulated genes were altered through the nicotinic acetylcholine receptors (nAChRs)-mediated signaling process. We further identified 14 biochemical pathways enriched among the nicotine-modulated genes, among which were those involved in neural development/synaptic plasticity, neuronal survival/death, immune response, or cellular metabolism. In the genes significantly regulated by nicotine but blocked by mecamylamine, 13 enriched pathways were detected. Nine of these pathways were shared with those enriched in the genes regulated by nicotine, including neuronal function-related pathways such as glucocorticoid receptor signaling, p38 MAPK signaling, PI3K/AKT signaling, and PTEN signaling, implying that nAChRs play important roles in the regulation of these biological processes. Together, our results not only provide insights into the mechanism underlying the acute response of neuronal cells to nicotine but also provide clues to how acute nicotine exposure exerts long-term effects on the nervous system. PMID:21556275

  11. A markov classification model for metabolic pathways

    PubMed Central

    2010-01-01

    Background This paper considers the problem of identifying pathways through metabolic networks that relate to a specific biological response. Our proposed model, HME3M, first identifies frequently traversed network paths using a Markov mixture model. Then by employing a hierarchical mixture of experts, separate classifiers are built using information specific to each path and combined into an ensemble prediction for the response. Results We compared the performance of HME3M with logistic regression and support vector machines (SVM) for both simulated pathways and on two metabolic networks, glycolysis and the pentose phosphate pathway for Arabidopsis thaliana. We use AltGenExpress microarray data and focus on the pathway differences in the developmental stages and stress responses of Arabidopsis. The results clearly show that HME3M outperformed the comparison methods in the presence of increasing network complexity and pathway noise. Furthermore an analysis of the paths identified by HME3M for each metabolic network confirmed known biological responses of Arabidopsis. Conclusions This paper clearly shows HME3M to be an accurate and robust method for classifying metabolic pathways. HME3M is shown to outperform all comparison methods and further is capable of identifying known biologically active pathways within microarray data. PMID:20047667

  12. A novel signaling pathway impact analysis

    PubMed Central

    Tarca, Adi Laurentiu; Draghici, Sorin; Khatri, Purvesh; Hassan, Sonia S.; Mittal, Pooja; Kim, Jung-sun; Kim, Chong Jai; Kusanovic, Juan Pedro; Romero, Roberto

    2009-01-01

    Motivation: Gene expression class comparison studies may identify hundreds or thousands of genes as differentially expressed (DE) between sample groups. Gaining biological insight from the result of such experiments can be approached, for instance, by identifying the signaling pathways impacted by the observed changes. Most of the existing pathway analysis methods focus on either the number of DE genes observed in a given pathway (enrichment analysis methods), or on the correlation between the pathway genes and the class of the samples (functional class scoring methods). Both approaches treat the pathways as simple sets of genes, disregarding the complex gene interactions that these pathways are built to describe. Results: We describe a novel signaling pathway impact analysis (SPIA) that combines the evidence obtained from the classical enrichment analysis with a novel type of evidence, which measures the actual perturbation on a given pathway under a given condition. A bootstrap procedure is used to assess the significance of the observed total pathway perturbation. Using simulations we show that the evidence derived from perturbations is independent of the pathway enrichment evidence. This allows us to calculate a global pathway significance P-value, which combines the enrichment and perturbation P-values. We illustrate the capabilities of the novel method on four real datasets. The results obtained on these data show that SPIA has better specificity and more sensitivity than several widely used pathway analysis methods. Availability: SPIA was implemented as an R package available at http://vortex.cs.wayne.edu/ontoexpress/ Contact: sorin@wayne.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:18990722

  13. Interactive Fly: Developmental Pathways

    NSDL National Science Digital Library

    PhD Thomas B Brody (NIH Laboratory of Neurochemistry)

    2006-12-11

    this site describes evolutionarily conserved developmental pathways. The pathways are named according to the processes they govern, and not by the names of the genes involved: for example, "lateral inhibition" rather than "the Notch pathway." Inevitably, there will be cases where the function is less well understood: hence, "the Wingless pathway."

  14. A systems biology approach for pathway level analysis

    Microsoft Academic Search

    Sorin Draghici; Purvesh Khatri; Adi Laurentiu Tarca; Kashyap Amin; Arina Done; Calin Voichita; Constantin Georgescu; Roberto Romero

    2007-01-01

    A common challenge in the analysis of genomics data is trying to understand the underlying phenomenon in the context of all complex interactions taking place on various signaling pathways. A statistical approach using various models is universally used to identify the most relevant pathways in a given experiment. Here, we show that the existing pathway analysis methods fail to take

  15. High-Performance Photovoltaic Project: Identifying Critical Pathways; Kickoff Meeting

    SciTech Connect

    Symko-Davis, M.

    2001-11-07

    The High Performance Photovoltaic Project held a Kickoff Meeting in October, 2001. This booklet contains the presentations given by subcontractors and in-house teams at that meeting. The areas of subcontracted research under the HiPer project include Polycrystalline Thin Films and Multijunction Concentrators. The in-house teams in this initiative will focus on three areas: (1) High-Performance Thin-Film Team-leads the investigation of tandem structures and low-flux concentrators, (2) High-Efficiency Concepts and Concentrators Team-an expansion of an existing team that leads the development of high-flux concentrators, and (3) Thin-Film Process Integration Team-will perform fundamental process and characterization research, to resolve the complex issues of making thin-film multijunction devices.

  16. Biochemical analysis of germination mutants to characterize germinant receptors of Bacillus subtilis 1604 spores.

    PubMed

    Venkatasubramanian, P; Johnstone, K

    1993-08-01

    Spores of Bacillus subtilis 1604 can be induced to germinate by incubation in L-Ala (the ALA pathway) or in a combination of beta-D-glucose (Glc), beta-fructose (Fru), L-Asn and K+ (the GFAK pathway). Biochemical analysis of the germination response of a gerA mutant deficient in the ALA pathway revealed that L-Ala can replace L-Asn in the GFAK pathway (the GFAlaK pathway). In contrast to the ALA pathway of both the wild-type and of a gerB mutant, the GFAlaK pathway was insensitive to D-Ala and showed the same overall inhibitor profile as the GFAK pathway of wild-type and gerA spores. It is deduced that a second L-Ala receptor with different characteristics to that functioning in the ALA pathway is present in wild-type spores. Analysis of the germination response of a gerB mutant showed that whilst the rate of ALA germination could be stimulated by Glc as well as by Fru in the presence of Glc, the spores could not germinate in GFAK. In addition, Glc and Fru were unable to reverse D-Ala inhibition of L-Ala germination which they do in the wild-type. Thus, in the gerB mutant, the L-Ala/L-Asn receptor in the GFAK pathway is defective. It is concluded that the germination receptors in the ALA and GFAK pathways can functionally interact with each other to initiate B. subtilis spore germination. This conclusion is discussed in relation to proposed models of triggering of spore germination. PMID:8409928

  17. Biochemical Applications in the Analytical Chemistry Lab

    NASA Astrophysics Data System (ADS)

    Strong, Cynthia; Ruttencutter, Jeffrey

    2004-12-01

    In response to the increasing importance of biochemical applications in modern analytical chemistry and the high level of interest in biochemistry among students at Cornell College, we sought to incorporate more biochemical concepts and methods into the sophomore-level analytical course. This report describes bioanalyical experiments that have been developed or adapted using an HPLC and a UV visible spectrophotometer. Specific experiments include amino acid analysis, biochromatography, and total protein analysis. These improvements have the potential to increase our students' understanding of selected biochemistry topics and enhance their ability to apply an analytical approach to solving biochemical problems.

  18. [Biochemical markers of iron status].

    PubMed

    Aimone-Gastin, Isabelle

    2006-11-01

    Traditionally, the standard biochemical markers of iron status are serum iron, transferrin, transferrin saturation, ferritin and, more recently, soluble transferrin receptor. Diagnosis of iron deficiency is usually associated with a low serum ferritin concentration. The diagnosis can be difficult in diseases in which there is an acute-phase response, because ferritin is an acute-phase reactant. In this case, measuring soluble transferrin receptor may be useful because an increased concentration is an indicator of iron deficiency. Iron stores are frequently diminished in patients on dialysis, as a result of increased blood loss and poor iron absorption. Demand for available iron is increased further by the use of erythropoietin and iron deficiency is one of the primary causes for decreased response to recombinant human erythropoeitin therapy (rHuEpo). Prevalence of inflammation in patients on dialysis is estimated to be high (as 50% patients). Because ferritin is an acute-phase reactant, levels may be elevated in cases of inflammation. The aim of recent guidelines is to better assess anaemia and iron stores. Serum ferritin and transferrin saturation are regarded as the most reliable indicators of iron status. A newer alternative laboratory measurement is the soluble transferrin receptor. Some authors suggest that the circulating soluble transferring receptor levels may be useful in monitoring iron status in patients on dialysis if rHuEpo doses are maintained constant. Prospective longitudinal studies are needed to evaluate this hypothesis. PMID:17373277

  19. GPU accelerated biochemical network simulation

    PubMed Central

    Zhou, Yanxiang; Liepe, Juliane; Sheng, Xia; Stumpf, Michael P. H.; Barnes, Chris

    2011-01-01

    Motivation: Mathematical modelling is central to systems and synthetic biology. Using simulations to calculate statistics or to explore parameter space is a common means for analysing these models and can be computationally intensive. However, in many cases, the simulations are easily parallelizable. Graphics processing units (GPUs) are capable of efficiently running highly parallel programs and outperform CPUs in terms of raw computing power. Despite their computational advantages, their adoption by the systems biology community is relatively slow, since differences in hardware architecture between GPUs and CPUs complicate the porting of existing code. Results: We present a Python package, cuda-sim, that provides highly parallelized algorithms for the repeated simulation of biochemical network models on NVIDIA CUDA GPUs. Algorithms are implemented for the three popular types of model formalisms: the LSODA algorithm for ODE integration, the Euler–Maruyama algorithm for SDE simulation and the Gillespie algorithm for MJP simulation. No knowledge of GPU computing is required from the user. Models can be specified in SBML format or provided as CUDA code. For running a large number of simulations in parallel, up to 360-fold decrease in simulation runtime is attained when compared to single CPU implementations. Availability: http://cuda-sim.sourceforge.net/ Contact: christopher.barnes@imperial.ac.uk; m.stumpf@imperial.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21224286

  20. Combining Flux Balance and Energy Balance Analysis for Large-Scale Metabolic Network: Biochemical Circuit Theory for Analysis of Large-Scale Metabolic Networks

    NASA Technical Reports Server (NTRS)

    Beard, Daniel A.; Liang, Shou-Dan; Qian, Hong; Biegel, Bryan (Technical Monitor)

    2001-01-01

    Predicting behavior of large-scale biochemical metabolic networks represents one of the greatest challenges of bioinformatics and computational biology. Approaches, such as flux balance analysis (FBA), that account for the known stoichiometry of the reaction network while avoiding implementation of detailed reaction kinetics are perhaps the most promising tools for the analysis of large complex networks. As a step towards building a complete theory of biochemical circuit analysis, we introduce energy balance analysis (EBA), which compliments the FBA approach by introducing fundamental constraints based on the first and second laws of thermodynamics. Fluxes obtained with EBA are thermodynamically feasible and provide valuable insight into the activation and suppression of biochemical pathways.

  1. An extracellular disulfide bond forming protein (DsbF) from Mycobacterium tuberculosis: Structural, biochemical and gene expression analysis

    PubMed Central

    Chim, Nicholas; Riley, Robert; The, Juliana; Im, Soyeon; Segelke, Brent; Lekin, Tim; Yu, Minmin; Hung, Li Wei; Terwilliger, Tom; Whitelegge, Julian P.; Goulding, Celia W.

    2010-01-01

    Disulfide bond forming (Dsb) proteins ensure correct folding and disulfide bond formation of secreted proteins. Previously, we showed that Mycobacterium tuberculosis DsbE (Mtb DsbE, Rv2878c) aids in vitro oxidative folding of proteins. Here we present structural, biochemical and gene expression analyses of another putative Mtb secreted disulfide bond isomerase protein homologous to Mtb DsbE, Mtb DsbF (Rv1677). The X-ray crystal structure of Mtb DsbF reveals a conserved thioredoxin fold although the active-site cysteines may be modeled in both oxidized and reduced forms, in contrast to the solely reduced form in Mtb DsbE. Furthermore, the shorter loop region in Mtb DsbF results in a more solvent-exposed active site. Biochemical analyses show that, similar to Mtb DsbE, Mtb DsbF can oxidatively refold reduced, unfolded hirudin and has a comparable pKa for the active-site solvent-exposed cysteine. However, contrary to Mtb DsbE, the Mtb DsbF redox potential is more oxidizing and its reduced state is more stable. From computational genomics analysis of the M. tuberculosis genome, we identified a potential Mtb DsbF interaction partner, Rv1676, a predicted peroxiredoxin. Complex formation is supported by protein co-expression studies and inferred by gene expression profiles, whereby Mtb DsbF and Rv1676 are upregulated under similar environments. Additionally, comparison of Mtb DsbF and Mtb DsbE gene expression data indicate anticorrelated gene expression patterns, suggesting that these two proteins and their functionally linked partners constitute analogous pathways that may function under different conditions. PMID:20060836

  2. Arabidopsis Jasmonate Signaling Pathway

    NSDL National Science Digital Library

    Aurelie Gfeller (University of Lausanne; Gene Expression Laboratory and Faculty of Biology and Medicine REV)

    2006-02-14

    Jasmonates control defense gene expression and male fertility in the model plant Arabidopsis thaliana. In both cases, the involvement of the jasmonate pathway is complex, involving large-scale transcriptional reprogramming. Additionally, jasmonate signaling is hard-wired into the auxin, ethylene, and salicylate signal networks, all of which are under intense investigation in Arabidopsis. In male fertility, jasmonic acid (JA) is the essential signal intervening both at the level of anther elongation and in pollen dehiscense. A number of genes potentially involved in jasmonate-dependent anther elongation have recently been discovered. In the case of defense, at least two jasmonates, JA and its precursor 12-oxo-phytodienoic acid (OPDA), are necessary for the fine-tuning of defense gene expression in response to various microbial pathogens and arthropod herbivores. However, only OPDA is required for full resistance to some insects and fungi. Other jasmonates probably affect yet more physiological responses. A series of breakthroughs have identified the SKP/CULLIN/F-BOX (SCF), CORONATINE INSENSITIVE (COI1) complex, acting together with the CONSTITUTIVE PHOTOMORPHOGENIC 9 (COP9) signalosome, as central regulatory components of jasmonate signaling in Arabidopsis. The studies, mostly involving mutational approaches, have paved the way for suppressor screens that are expected to further extend our knowledge of jasmonate signaling. When these and other new mutants affecting jasmonate signaling are characterized, new nodes will be added to the Arabidopsis Jasmonate Signaling Pathway Connections Map, and the lists of target genes regulated by jasmonates in Arabidopsis will be expanded.

  3. Global transcriptome analysis of formalin-fixed prostate cancer specimens identifies biomarkers of disease recurrence

    PubMed Central

    Long, Qi; Xu, Jianpeng; Osunkoya, Adeboye O.; Sannigrahi, Soma; Johnson, Brent A.; Zhou, Wei; Gillespie, Theresa; Park, Jong Y.; Nam, Robert K.; Sugar, Linda; Stanimirovic, Aleksandra; Seth, Arun K.; Petros, John A.; Moreno, Carlos S.

    2014-01-01

    Prostate cancer remains the second leading cause of cancer death in American men and there is an unmet need for biomarkers to identify patients with aggressive disease. In an effort to identify biomarkers of recurrence, we performed global RNA sequencing on 106 formalin-fixed, paraffin-embedded (FFPE) prostatectomy samples from 100 patients at three independent sites, defining a 24-gene signature panel. The 24 genes in this panel function in cell cycle progression, angiogenesis, hypoxia, apoptosis, PI3K signaling, steroid metabolism, translation, chromatin modification and transcription. Sixteen genes have been associated with cancer with five specifically associated with prostate cancer (BTG2, IGFBP3, SIRT1, MXI1 and FDPS). Validation was performed on an independent publicly available dataset of 140 patients, where the new signature panel outperformed markers published previously in terms of predicting biochemical recurrence (BCR). Our work also identified differences in gene expression between Gleason Pattern 4+3 and 3+4 tumors, including several genes involved in the epithelial to mesenchymal transition and developmental pathways. Overall, this study defines a novel biomarker panel that has the potential to improve the clinical management of prostate cancer. PMID:24713434

  4. Structural Organization of Enzymes of the Phenylacetate Catabolic Hybrid Pathway

    PubMed Central

    Grishin, Andrey M.; Cygler, Miroslaw

    2015-01-01

    Aromatic compounds are the second most abundant class of molecules on the earth and frequent environmental pollutants. They are difficult to metabolize due to an inert chemical structure, and of all living organisms, only microbes have evolved biochemical pathways that can open an aromatic ring and catabolize thus formed organic molecules. In bacterial genomes, the phenylacetate (PA) utilization pathway is abundant and represents the central route for degradation of a variety of organic compounds, whose degradation reactions converge at this pathway. The PA pathway is a hybrid pathway and combines the dual features of aerobic metabolism, i.e., usage of both oxygen to open the aromatic ring and of anaerobic metabolism—coenzyme A derivatization of PA. This allows the degradation process to be adapted to fluctuating oxygen conditions. In this review we focus on the structural and functional aspects of enzymes and their complexes involved in the PA degradation by the catabolic hybrid pathway. We discuss the ability of the central PaaABCE monooxygenase to reversibly oxygenate PA, the controlling mechanisms of epoxide concentration by the pathway enzymes, and the similarity of the PA utilization pathway to the benzoate utilization Box pathway and ?-oxidation of fatty acids. PMID:26075354

  5. Single-molecule detection: applications to ultrasensitive biochemical analysis

    NASA Astrophysics Data System (ADS)

    Castro, Alonso; Shera, E. Brooks

    1995-06-01

    Recent developments in laser-based detection of fluorescent molecules have made possible the implementation of very sensitive techniques for biochemical analysis. We present and discuss our experiments on the applications of our recently developed technique of single-molecule detection to the analysis of molecules of biological interest. These newly developed methods are capable of detecting and identifying biomolecules at the single-molecule level of sensitivity. In one case, identification is based on measuring fluorescence brightness from single molecules. In another, molecules are classified by determining their electrophoretic velocities.

  6. A Program on Biochemical and Biomedical Engineering.

    ERIC Educational Resources Information Center

    San, Ka-Yiu; McIntire, Larry V.

    1989-01-01

    Presents an introduction to the Biochemical and Biomedical Engineering program at Rice University. Describes the development of the academic and enhancement programs, including organizational structure and research project titles. (YP)

  7. The Diffusion Mediated Biochemical Signal Relay Channel

    E-print Network

    Thomas, Peter J.

    The Diffusion Mediated Biochemical Signal Relay Channel Peter J. Thomas , Donald J. Spencer localization by the immune system, Corresponding author: pjthomas@salk.edu dspencer@salk.edu #12;growth-cone

  8. Design guidelines for optical resonator biochemical sensors

    E-print Network

    Kimerling, Lionel C.

    In this paper, we propose a design tool for dielectric optical resonator-based biochemical refractometry sensors. Analogous to the widely accepted photodetector figure of merit, the detectivity D*, we introduce a new sensor ...

  9. MP-Align: alignment of metabolic pathways

    PubMed Central

    2014-01-01

    Background Comparing the metabolic pathways of different species is useful for understanding metabolic functions and can help in studying diseases and engineering drugs. Several comparison techniques for metabolic pathways have been introduced in the literature as a first attempt in this direction. The approaches are based on some simplified representation of metabolic pathways and on a related definition of a similarity score (or distance measure) between two pathways. More recent comparative research focuses on alignment techniques that can identify similar parts between pathways. Results We propose a methodology for the pairwise comparison and alignment of metabolic pathways that aims at providing the largest conserved substructure of the pathways under consideration. The proposed methodology has been implemented in a tool called MP-Align, which has been used to perform several validation tests. The results showed that our similarity score makes it possible to discriminate between different domains and to reconstruct a meaningful phylogeny from metabolic data. The results further demonstrate that our alignment algorithm correctly identifies subpathways sharing a common biological function. Conclusion The results of the validation tests performed with MP-Align are encouraging. A comparison with another proposal in the literature showed that our alignment algorithm is particularly well-suited to finding the largest conserved subpathway of the pathways under examination. PMID:24886436

  10. Enhancing a Pathway-Genome Database (PGDB) to Capture Subcellular Localization of Metabolites and Enzymes: The Nucleotide-Sugar Biosynthetic Pathways of Populus trichocarpa

    SciTech Connect

    Nag, A.; Karpinets, T. V.; Chang, C. H.; Bar-Peled, M.

    2012-01-01

    Understanding how cellular metabolism works and is regulated requires that the underlying biochemical pathways be adequately represented and integrated with large metabolomic data sets to establish a robust network model. Genetically engineering energy crops to be less recalcitrant to saccharification requires detailed knowledge of plant polysaccharide structures and a thorough understanding of the metabolic pathways involved in forming and regulating cell-wall synthesis. Nucleotide-sugars are building blocks for synthesis of cell wall polysaccharides. The biosynthesis of nucleotide-sugars is catalyzed by a multitude of enzymes that reside in different subcellular organelles, and precise representation of these pathways requires accurate capture of this biological compartmentalization. The lack of simple localization cues in genomic sequence data and annotations however leads to missing compartmentalization information for eukaryotes in automatically generated databases, such as the Pathway-Genome Databases (PGDBs) of the SRI Pathway Tools software that drives much biochemical knowledge representation on the internet. In this report, we provide an informal mechanism using the existing Pathway Tools framework to integrate protein and metabolite sub-cellular localization data with the existing representation of the nucleotide-sugar metabolic pathways in a prototype PGDB for Populus trichocarpa. The enhanced pathway representations have been successfully used to map SNP abundance data to individual nucleotide-sugar biosynthetic genes in the PGDB. The manually curated pathway representations are more conducive to the construction of a computational platform that will allow the simulation of natural and engineered nucleotide-sugar precursor fluxes into specific recalcitrant polysaccharide(s).

  11. Establishment of pomegranate (Punica granatum) hairy root cultures for genetic interrogation of the hydrolyzable tannin biosynthetic pathway.

    PubMed

    Ono, Nadia N; Bandaranayake, Pradeepa C G; Tian, Li

    2012-09-01

    In contrast to the numerous reports on the human therapeutic applications of hydrolyzable tannins (HTs), genes involved in their biosynthesis have not been identified at the molecular level from any plant species. Although we have previously identified candidate HT biosynthetic genes in pomegranate using transcriptomic and bioinformatic analyses, characterization of in planta enzyme function remains a critical step in biochemical pathway elucidation. We here report the establishment of a pomegranate (Punica granatum) hairy root culture system that produces HTs. Agrobacterium rhizogenes strains transformed with a binary vector harboring a yellow fluorescent protein (YFP) gene were used for hairy root induction, allowing visual, non-destructive, detection of transgene incorporation. It also demonstrated that the pomegranate hairy root culture system is suitable for expressing heterologous genes (YFP in this case). Expression of 26 putative UDP-glycosyltransferase (UGT) genes, obtained from a pomegranate fruit peel (a tissue highly abundant in HTs) RNA-Seq library, were verified in wild type and hairy roots. In addition, two candidate UGTs for HT biosynthesis were identified based on HPLC and differential gene expression analyses of various pomegranate tissues. Together with in vitro enzyme activity assays, the hairy root culture system holds great promise for revealing the undivulged HT biosynthetic pathway using pomegranate as a model system. PMID:22810948

  12. [Biochemical diagnostics of fatal opium intoxication].

    PubMed

    Papyshev, I P; Astashkina, O G; Tuchik, E S; Nikolaev, B S; Cherniaev, A L

    2013-01-01

    Biochemical diagnostics of fatal opium intoxication remains a topical problem in forensic medical science and practice. We investigated materials obtained in the course of forensic medical expertise of the cases of fatal opium intoxication. The study revealed significant differences between myoglobin levels in blood, urine, myocardium, and skeletal muscles. The proposed approach to biochemical diagnostics of fatal opium intoxication enhances the accuracy and the level of evidence of expert conclusions. PMID:23802303

  13. Early transcriptional response to aminoglycoside antibiotic suggests alternate pathways leading to apoptosis in sensory hair cells in the mouse inner ear

    PubMed Central

    Tao, Litao; Segil, Neil

    2015-01-01

    Aminoglycoside antibiotics are “the drug of choice” for treating many bacterial infections, but their administration results in hearing loss in up to one fourth of the patients who receive them. Several biochemical pathways have been implicated in aminoglycoside antibiotic ototoxicity; however, little is known about how hair cells respond to aminoglycoside antibiotics at the transcriptome level. Here we have investigated the genome-wide response to the aminoglycoside antibiotic gentamicin. Using organotypic cultures of the perinatal organ of Corti, we performed RNA sequencing using cDNA libraries obtained from FACS-purified hair cells. Within 3 h of gentamicin treatment, the messenger RNA level of more than three thousand genes in hair cells changed significantly. Bioinformatic analysis of these changes highlighted several known signal transduction pathways, including the JNK pathway and the NF-?B pathway, in addition to genes involved in the stress response, apoptosis, cell cycle control, and DNA damage repair. In contrast, only 698 genes, mainly involved in cell cycle and metabolite biosynthetic processes, were significantly affected in the non-hair cell population. The gene expression profiles of hair cells in response to gentamicin share a considerable similarity with those previously observed in gentamicin-induced nephrotoxicity. Our findings suggest that previously observed early responses to gentamicin in hair cells in specific signaling pathways are reflected in changes in gene expression. Additionally, the observed changes in gene expression of cell cycle regulatory genes indicate a disruption of the postmitotic state, which may suggest an alternate pathway regulating gentamicin-induced apoptotic hair cell death. This work provides a more comprehensive view of aminoglycoside antibiotic ototoxicity, and thus contributes to identifying potential pathways or therapeutic targets to alleviate this important side effect of aminoglycoside antibiotics. PMID:26052268

  14. Associative learning in biochemical networks

    E-print Network

    Nikhil Ghandi; Gonen Ashkenasy; Emmanuel Tannenbaum

    2007-01-04

    We develop a simple, chemostat-based model illustrating how a process analogous to associative learning can occur in a biochemical network. Associative learning is a form of learning whereby a system "learns" to associate two stimuli with one another. In our model, two types of replicating molecules, denoted A and B, are present in some initial concentration in the chemostat. Molecules A and B are stimulated to replicate by some growth factors, denoted GA and GB, respectively. It is also assumed that A and B can covalently link, and that the conjugated molecule can be stimulated by either the GA or GB growth factors (and can be degraded). We show that, if the chemostat is stimulated by both growth factors for a certain time, followed by a time gap during which the chemostat is not stimulated at all, and if the chemostat is then stimulated again by only one of the growth factors, then there will be a transient increase in the number of molecules activated by the other growth factor. Therefore, the chemostat bears the imprint of earlier, simultaneous stimulation with both growth factors, which is indicative of associative learning. It is interesting to note that the dynamics of our model is consistent with various aspects of Pavlov's original series of associative learning experiments in dogs. We discuss how associative learning can potentially be performed in vitro within RNA, DNA, or peptide networks. We also highlight how such a mechanism could potentially be involved in genomic evolution, and suggest bioinformatics studies that could be used to find evidence for associative learning processes at work inside living cells.

  15. Exploring pathway interactions in insulin resistant mouse liver

    PubMed Central

    2011-01-01

    Background Complex phenotypes such as insulin resistance involve different biological pathways that may interact and influence each other. Interpretation of related experimental data would be facilitated by identifying relevant pathway interactions in the context of the dataset. Results We developed an analysis approach to study interactions between pathways by integrating gene and protein interaction networks, biological pathway information and high-throughput data. This approach was applied to a transcriptomics dataset to investigate pathway interactions in insulin resistant mouse liver in response to a glucose challenge. We identified regulated pathway interactions at different time points following the glucose challenge and also studied the underlying protein interactions to find possible mechanisms and key proteins involved in pathway cross-talk. A large number of pathway interactions were found for the comparison between the two diet groups at t = 0. The initial response to the glucose challenge (t = 0.6) was typed by an acute stress response and pathway interactions showed large overlap between the two diet groups, while the pathway interaction networks for the late response were more dissimilar. Conclusions Studying pathway interactions provides a new perspective on the data that complements established pathway analysis methods such as enrichment analysis. This study provided new insights in how interactions between pathways may be affected by insulin resistance. In addition, the analysis approach described here can be generally applied to different types of high-throughput data and will therefore be useful for analysis of other complex datasets as well. PMID:21843341

  16. Plant glutathione biosynthesis: diversity in biochemical regulation and reaction products.

    PubMed

    Galant, Ashley; Preuss, Mary L; Cameron, Jeffrey C; Jez, Joseph M

    2011-01-01

    In plants, exposure to temperature extremes, heavy metal-contaminated soils, drought, air pollutants, and pathogens results in the generation of reactive oxygen species that alter the intracellular redox environment, which in turn influences signaling pathways and cell fate. As part of their response to these stresses, plants produce glutathione. Glutathione acts as an anti-oxidant by quenching reactive oxygen species, and is involved in the ascorbate-glutathione cycle that eliminates damaging peroxides. Plants also use glutathione for the detoxification of xenobiotics, herbicides, air pollutants (sulfur dioxide and ozone), and toxic heavy metals. Two enzymes catalyze glutathione synthesis: glutamate-cysteine ligase, and glutathione synthetase. Glutathione is a ubiquitous protective compound in plants, but the structural and functional details of the proteins that synthesize it, as well as the potential biochemical mechanisms of their regulation, have only begun to be explored. As discussed here, the core reactions of glutathione synthesis are conserved across various organisms, but plants have diversified both the regulatory mechanisms that control its synthesis and the range of products derived from this pathway. Understanding the molecular basis of glutathione biosynthesis and its regulation will expand our knowledge of this component in the plant stress response network. PMID:22645536

  17. Working Together for Children: Strengthening Transition Pathways

    ERIC Educational Resources Information Center

    Collie, Louise; Willis, Felicity; Paine, Crystal; Windsor, Corina

    2007-01-01

    The "Working Together for Children: Strengthening Transition Pathways" Team has identified that there is a gap between the Early Childhood settings and schools within the Dubbo area. Through meetings with early childhood professionals within Dubbo the authors have identified that the current landscape of care and education within their community…

  18. Biochemical markers of ongoing joint damage in rheumatoid arthritis - current and future applications, limitations and opportunities

    PubMed Central

    2011-01-01

    Rheumatoid arthritis (RA) is a chronic systemic autoimmune disease associated with potentially debilitating joint inflammation, as well as altered skeletal bone metabolism and co-morbid conditions. Early diagnosis and aggressive treatment to control disease activity offers the highest likelihood of preserving function and preventing disability. Joint inflammation is characterized by synovitis, osteitis, and/or peri-articular osteopenia, often accompanied by development of subchondral bone erosions, as well as progressive joint space narrowing. Biochemical markers of joint cartilage and bone degradation may enable timely detection and assessment of ongoing joint damage, and their use in facilitating treatment strategies is under investigation. Early detection of joint damage may be assisted by the characterization of biochemical markers that identify patients whose joint damage is progressing rapidly and who are thus most in need of aggressive treatment, and that, alone or in combination, identify those individuals who are likely to respond best to a potential treatment, both in terms of limiting joint damage and relieving symptoms. The aims of this review are to describe currently available biochemical markers of joint metabolism in relation to the pathobiology of joint damage and systemic bone loss in RA; to assess the limitations of, and need for additional, novel biochemical markers in RA and other rheumatic diseases, and the strategies used for assay development; and to examine the feasibility of advancement of personalized health care using biochemical markers to select therapeutic agents to which a patient is most likely to respond. PMID:21539724

  19. Manipulating Natural Product Biosynthetic Pathways via DNA Assembler

    PubMed Central

    Shao, Zengyi; Zhao, Huimin

    2014-01-01

    DNA assembler is an efficient synthetic biology method for constructing and manipulating biochemical pathways. The rapidly increasing number of sequenced genomes provides a rich source for discovery of gene clusters involved in synthesizing new natural products. However, both discovery and economical production are hampered by our limited knowledge in manipulating most organisms and the corresponding pathways. By taking advantage of yeast in vivo homologous recombination, DNA assembler synthesizes an entire expression vector containing the target biosynthetic pathway and the genetic elements needed for DNA maintenance and replication. Here we use the spectinabilin clusters originated from two hosts as examples to illustrate the guidelines of using DNA assembler for cluster characterization and silent cluster activation. Such strategies offer unprecedented versatility in cluster manipulation, bypass the traditional laborious strategies to elicit pathway expression, and provide a new platform for de novo cluster assembly and genome mining for discovering new natural products. PMID:24903884

  20. Host Glycan Sugar-Specific Pathways in Streptococcus pneumonia: Galactose as a Key Sugar in Colonisation and Infection

    PubMed Central

    Paixão, Laura; Oliveira, Joana; Veríssimo, André; Vinga, Susana; Lourenço, Eva C.; Ventura, M. Rita; Kjos, Morten; Veening, Jan-Willem; Fernandes, Vitor E.; Andrew, Peter W.; Yesilkaya, Hasan; Neves, Ana Rute

    2015-01-01

    The human pathogen Streptococcus pneumoniae is a strictly fermentative organism that relies on glycolytic metabolism to obtain energy. In the human nasopharynx S. pneumoniae encounters glycoconjugates composed of a variety of monosaccharides, which can potentially be used as nutrients once depolymerized by glycosidases. Therefore, it is reasonable to hypothesise that the pneumococcus would rely on these glycan-derived sugars to grow. Here, we identified the sugar-specific catabolic pathways used by S. pneumoniae during growth on mucin. Transcriptome analysis of cells grown on mucin showed specific upregulation of genes likely to be involved in deglycosylation, transport and catabolism of galactose, mannose and N acetylglucosamine. In contrast to growth on mannose and N-acetylglucosamine, S. pneumoniae grown on galactose re-route their metabolic pathway from homolactic fermentation to a truly mixed acid fermentation regime. By measuring intracellular metabolites, enzymatic activities and mutant analysis, we provide an accurate map of the biochemical pathways for galactose, mannose and N-acetylglucosamine catabolism in S. pneumoniae. Intranasal mouse infection models of pneumococcal colonisation and disease showed that only mutants in galactose catabolic genes were attenuated. Our data pinpoint galactose as a key nutrient for growth in the respiratory tract and highlights the importance of central carbon metabolism for pneumococcal pathogenesis. PMID:25826206

  1. A kinome-wide siRNA screen identifies multiple roles for protein kinases in hypoxic stress adaptation, including roles for IRAK4 and GAK in protection against apoptosis in VHL-/- renal carcinoma cells, despite activation of the NF-?B pathway.

    PubMed

    Pan, Jing; Zhang, Jing; Hill, Andrew; Lapan, Peter; Berasi, Steve; Bates, Brian; Miller, Christopher; Haney, Steven

    2013-08-01

    Hypoxia induces changes to cancer cells that make them more resistant to treatment. We have looked at signaling pathways that facilitate these changes by screening the human kinome for effects on hypoxic responses in SW480 colon cancer cells. Hits identified in the screen were examined for effects on multiple molecular responses to hypoxia, including the endoplasmic reticulum stress and DNA damage responses in colon, melanoma, and renal cancer lines. To validate the hits from the small interfering RNA studies, we developed cell lines expressing stable short hairpin RNAs (shRNAs) in the A498 renal carcinoma cell line. Several lines, including those expressing shRNAs against DYRK1B, GAK, IHPK2, IRAK4, and MATK, showed an inability to form spheroid cultures. In addition, shRNAs targeting IRAK4 and GAK were incapable of 2D growth under anoxia. In the GAK shRNA-expressing line, nuclear factor-?B (NF-?B) was localized to the nucleus, but in the IRAK4 shRNA line, NF-?B levels were increased but the extent of nuclear localization was unchanged. Dominant negative mutants of IRAK4 and GAK also showed strong apoptotic effects in A498 cells under anoxia, supporting a direct link between these kinases and survival of the VHL(-/-) RCC line, which is typically highly resistant to hypoxic stress as a result of high and constitutive levels of Hif-1?. PMID:23591012

  2. What is the Hippo pathway? Is the Hippo pathway conserved in Caenorhabditis elegans?

    PubMed

    Yang, Zeyu; Hata, Yutaka

    2013-09-01

    The Hippo pathway was originally identified in Drosophila as the signalling pathway that governs organ size. The core of the pathway harbours two protein kinases (Hippo and Warts). Hippo phosphorylates and activates Warts, which in turn phosphorylates and inactivates the transcriptional co-activator Yorkie. As Yorkie mediates cell cycle-promoting and anti-apoptotic gene transcriptions, the Hippo pathway suppresses cell cycle progression and induces apoptosis. The pathway was named after Hippo, which was regarded as a key component. The pathway was initially considered to be well conserved in mammals. Indeed the mammalian homologues of Hippo, and Warts negatively regulate Yorkie homologue and function as the tumour suppressors. However, the researchers have identified numerous additional components both in Drosophila and mammals and the significant interspecies diversity is now evident. To make things more complicated, the regulation of the pathway does not necessarily depend on Hippo homologues. In this commentary, we reconsider what is essential for the Hippo pathway and try to sort out the controversial arguments in the discussion of the evolutionary root of the pathway. PMID:23843471

  3. Immunocytochemical and biochemical identification of angiotensin II in human nasal tissue

    Microsoft Academic Search

    P Ostertag; B Mack; G Rasp; K Hermann

    2002-01-01

    Angiotensin II (ANG II) was identified immunocytochemically and biochemically in biopsy samples of human nasal tissue. Staining for ANG II was predominantly found in structures similar to a string of pearls with consecutive short varicose areas, which is characteristic for neuronal tissue. The localization of ANG II in neurons was confirmed by positive staining of adjacent tissue sections with a

  4. Biochemical (Prostate Specific Antigen) Recurrence Probability Following Radical Prostatectomy for Clinically Localized Prostate Cancer

    Microsoft Academic Search

    MISOP HAN; ALAN W. PARTIN; MARIANNA ZAHURAK; STEVEN PIANTADOSI; JONATHAN I. EPSTEIN; PATRICK C. WALSH

    2003-01-01

    PurposeWe retrospectively reviewed the clinical followup for a large series of men with clinically localized prostate cancer who underwent radical retropubic prostatectomy to identify clinical and\\/or pathological indicators of biochemical (prostate specific antigen [PSA]) recurrence. We then used those indicators to develop multivariate models for determination of recurrence probability following radical retropubic prostatectomy.

  5. Biochemical and Spectroscopic Characterization of the Covalent Binding of Heme to Cytochrome b6

    E-print Network

    Biochemical and Spectroscopic Characterization of the Covalent Binding of Heme to Cytochrome b6 of the cytochrome b6f complex disclosed the unexpected presence of a new heme ci [Stroebel, D., Choquet, Y., Popot identify a Cys35-containing proteolytic fragment (Tyr25-Lys111) from cytochrome b6 as a peptide

  6. COMBINED USE OF BIOCHEMICAL INDICATORS TO ASSESS SUBLETHAL POLLUTION EFFECTS ON THE GULF KILLIFISH ('FUNDULUS GRANDIS')

    EPA Science Inventory

    Sublethal biochemical markers were used to identify liver enzyme induction in fish from a bayou in Pensacola, Florida. Gulf killifish, Fundulus grandis, from a nonpolluted site were used in the study which included laboratory-induced fish and their various controls as well as the...

  7. Biological pathways as communicating computer systems.

    PubMed

    Kwiatkowska, Marta Z; Heath, John K

    2009-08-15

    Time and cost are the enemies of cell biology. The number of experiments required to rigorously dissect and comprehend a pathway of even modest complexity is daunting. Methods are needed to formulate biological pathways in a machine-analysable fashion, which would automate the process of considering all possible experiments in a complex pathway and identify those that command attention. In this Essay, we describe a method that is based on the exploitation of computational tools that were originally developed to analyse reactive communicating computer systems such as mobile phones and web browsers. In this approach, the biological process is articulated as an executable computer program that can be interrogated using methods that were developed to analyse complex software systems. Using case studies of the FGF, MAPK and Delta/Notch pathways, we show that the application of this technology can yield interesting insights into the behaviour of signalling pathways, which have subsequently been corroborated by experimental data. PMID:19657015

  8. The analytical determination of isoprenoid intermediates from the mevalonate pathway

    Microsoft Academic Search

    Gudrun Nürenberg; Dietrich A. Volmer

    In this article, assays on the analytical determination of farnesyl pyrophosphate (FPP) and geranylgeranyl pyrophosphate (GGPP),\\u000a two important isoprenoid intermediates at biochemically relevant branching points in the mevalonate pathway, are summarized\\u000a and reviewed. There is considerable recent interest in the measurement of these two isoprenoids because of their direct involvement\\u000a in several diseases, for example, statins lower cholesterol by inhibiting

  9. The Pathway Tools cellular overview diagram and Omics Viewer

    PubMed Central

    Paley, Suzanne M.; Karp, Peter D.

    2006-01-01

    The Pathway Tools cellular overview diagram is a visual representation of the biochemical network of an organism. The overview is automatically created from a Pathway/Genome Database describing that organism. The cellular overview includes metabolic, transport and signaling pathways, and other membrane and periplasmic proteins. Pathway Tools supports interrogation and exploration of cellular biochemical networks through the overview diagram. Furthermore, a software component called the Omics Viewer provides visual analysis of whole-organism datasets using the overview diagram as an organizing framework. For example, gene expression and metabolomics measurements, alone or in combination, can be painted onto the overview, as can computed whole-organism datasets, such as predicted reaction-flux values. The cellular overview and Omics Viewer provide a mechanism whereby biologists can apply the pattern-recognition capabilities of the human visual system to analyze large-scale datasets in a biologically meaningful context. SRI's BioCyc.org website provides overview diagrams for more than 200 organisms. This article describes enhancements to the overview made since a 1999 publication, including the automatic layout capability, expansion of the cellular machinery that it includes, new semantic zooming and poster-generating capabilities, and extension of the Omics Viewer to support painting of metabolites, animations and zooming to individual pathway diagrams. PMID:16893960

  10. Genomic encyclopedia of sugar utilization pathways in the Shewanella genus

    SciTech Connect

    Rodionov, Dmitry A.; Yang, Chen; Li, Xiaoqing; Rodionova, Irina A.; Wang, Yanbing; Obraztsova, Anna; Zagnitko, Olga P.; Overbeek, Ross; Romine, Margaret F.; Reed, Samantha B.; Fredrickson, Jim K.; Nealson, Kenneth H.; Osterman, Andrei L.

    2010-09-13

    To address a practically and fundamentally important challenge of reconstruction of carbohydrate utilization machinery in any microorganism directly from its genomic sequence, we have established a subsystems-based comparative approach and applied it to 19 genomes from the Shewanella genus. The key stages of our approach include: (i) a homology-based identification of gene candidates using a genomic compilation of ~500 known components of sugar catabolic pathways; (ii) functional assignment of orthologs and prediction of alternative genes and pathway variants based on genomic (operons, regulons) and functional (subsystems, pathways) context analysis; (iii) validation of bioinformatic predictions by a combination of biochemical, genetic and physiological experiments. The obtained genomic encyclopedia of sugar utilization includes ~170 protein families (mostly metabolic enzymes, transporters and transcriptional regulators) spanning 17 distinct pathways with a mosaic distribution across Shewanella species providing insights into their ecophysiology and adaptive evolution. The reconstructed catabolic pathways are significantly enriched by nonorthologous gene replacements and alternative biochemical routes. Phenotypic assays revealed a remarkable consistency between predicted and observed phenotype, an ability to utilize an individual sugar as a sole source of carbon and energy, over the entire matrix of tested strains and sugars. In addition to improving our knowledge of genomics, functional organization and evolution of the sugar catabolome, this study confirmed the efficiency of the established approach, which is scalable and applicable to other groups of microorganisms.

  11. Calculation of control coefficients of metabolic pathways. A flux-oriented graph-theoretic approach.

    PubMed Central

    Sen, A K

    1991-01-01

    Within the premises of the flux-oriented theory of Crabtree & Newsholme [(1987) Biochem. J. 247, 113-120], I have used a graph-theoretic approach for calculating the Control Coefficients of metabolic pathways. It is shown that a directed graph representing the control structure of a metabolic pathway can be constructed in a heuristic manner directly from the reaction diagram of the pathway, without the necessity of writing down the governing equations for the Control Coefficients. The Control Coefficients are derived from an analysis of the topology of the directed graph. The graph-theoretic approach also provides a visual framework for analysing the functional relationships of the individual enzymes. The control structures of the following pathways are examined here: (a) a simple unbranched pathway with four enzymes, (b) a simple branched pathway with three enzymes, and (c) a branched pathway with both carbon and energy (ATP) fluxes. PMID:1930155

  12. Identifying genes affectng stress response in rainbow trout

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genomic analyses have the potential to impact aquaculture production traits by identifying markers as proxies for traits which are expensive or difficult to measure and characterizing genetic variation and biochemical mechanisms underlying phenotypic variation. One such set of traits are the respon...

  13. Completion of the seven-step pathway from tabersonine to the anticancer drug precursor vindoline and its assembly in yeast

    PubMed Central

    Qu, Yang; Easson, Michael L. A. E.; Froese, Jordan; Simionescu, Razvan; Hudlicky, Tomas; De Luca, Vincenzo

    2015-01-01

    Antitumor substances related to vinblastine and vincristine are exclusively found in the Catharanthus roseus (Madagascar periwinkle), a member of the Apocynaceae plant family, and continue to be extensively used in cancer chemotherapy. Although in high demand, these valuable compounds only accumulate in trace amounts in C. roseus leaves. Vinblastine and vincristine are condensed from the monoterpenoid indole alkaloid (MIA) precursors catharanthine and vindoline. Although catharanthine biosynthesis remains poorly characterized, the biosynthesis of vindoline from the MIA precursor tabersonine is well understood at the molecular and biochemical levels. This study uses virus-induced gene silencing (VIGS) to identify a cytochrome P450 [CYP71D1V2; tabersonine 3-oxygenase (T3O)] and an alcohol dehydrogenase [ADHL1; tabersonine 3-reductase (T3R)] as candidate genes involved in the conversion of tabersonine or 16-methoxytabersonine to 3-hydroxy-2,3-dihydrotabersonine or 3-hydroxy-16-methoxy-2,3-dihydrotabersonine, which are intermediates in the vindorosine and vindoline pathways, respectively. Biochemical assays with recombinant enzymes confirm that product formation is only possible by the coupled action of T3O and T3R, as the reaction product of T3O is an epoxide that is not used as a substrate by T3R. The T3O and T3R transcripts were identified in a C. roseus database representing genes preferentially expressed in leaf epidermis and suggest that the subsequent reaction products are transported from the leaf epidermis to specialized leaf mesophyll idioblast and laticifer cells to complete the biosynthesis of these MIAs. With these two genes, the complete seven-gene pathway was engineered in yeast to produce vindoline from tabersonine. PMID:25918424

  14. Biochemical systems identification by a random drift particle swarm optimization approach

    PubMed Central

    2014-01-01

    Background Finding an efficient method to solve the parameter estimation problem (inverse problem) for nonlinear biochemical dynamical systems could help promote the functional understanding at the system level for signalling pathways. The problem is stated as a data-driven nonlinear regression problem, which is converted into a nonlinear programming problem with many nonlinear differential and algebraic constraints. Due to the typical ill conditioning and multimodality nature of the problem, it is in general difficult for gradient-based local optimization methods to obtain satisfactory solutions. To surmount this limitation, many stochastic optimization methods have been employed to find the global solution of the problem. Results This paper presents an effective search strategy for a particle swarm optimization (PSO) algorithm that enhances the ability of the algorithm for estimating the parameters of complex dynamic biochemical pathways. The proposed algorithm is a new variant of random drift particle swarm optimization (RDPSO), which is used to solve the above mentioned inverse problem and compared with other well known stochastic optimization methods. Two case studies on estimating the parameters of two nonlinear biochemical dynamic models have been taken as benchmarks, under both the noise-free and noisy simulation data scenarios. Conclusions The experimental results show that the novel variant of RDPSO algorithm is able to successfully solve the problem and obtain solutions of better quality than other global optimization methods used for finding the solution to the inverse problems in this study. PMID:25078435

  15. MicroRNA-221 and -222 Regulate Radiation Sensitivity by Targeting the PTEN Pathway

    SciTech Connect

    Zhang Chunzhi [Department of Neurosurgery, Tianjin Medical University General Hospital, Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin 300052 (China); Department of Radiation Oncology, Tianjin Huan Hu Hospital, Tianjin 300060 (China); Kang Chunsheng [Department of Neurosurgery, Tianjin Medical University General Hospital, Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin 300052 (China); Wang Ping [Department of Radiation Oncology, Cancer Institute and Hospital of Tianjin Medical University, Tianjin 300060 (China); Cao Yongzhen; Lv Zhonghong [Department of Radiotherapy, Tianjin Medical University General Hospital, Tianjin 300052 (China); Yu Shizhu [Department of Neurology, Tianjin Medical University General Hospital, Laboratory of Neuro-pathology, Tianjin Neurological Institute, Tianjin 300052 (China); Wang Guangxiu; Zhang Anling; Jia Zhifan; Han Lei [Department of Neurosurgery, Tianjin Medical University General Hospital, Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin 300052 (China); Yang Chunying; Ishiyama, Hiromichi; Teh, Bin S. [Department of Radiation Oncology, Methodist Hospital Research Institute, Houston, Texas (United States); Xu Bo, E-mail: bxu@tmhs.or [Department of Radiation Oncology, Methodist Hospital Research Institute, Houston, Texas (United States); Pu Peiyu, E-mail: pupeiyu33@hotmail.co [Department of Neurosurgery, Tianjin Medical University General Hospital, Laboratory of Neuro-oncology, Tianjin Neurological Institute, Tianjin 300052 (China)

    2011-05-01

    Purpose: MicroRNAs (miRNAs) are noncoding RNAs inhibiting expression of numerous target genes by posttranscriptional regulation. miRNA-221 and miRNA-222 (miRNA-221/-222) expression is elevated in radioresistant tumor cell lines; however, it is not known whether and how miRNAs control cellular responses to ionizing irradiation. Methods and Materials: We used bioinformatic analyses, luciferase reporter assay, and genetic knockdown and biochemical assays to characterize the regulation pathways of miRNA-221/-222 in response to radiation treatment. Results: We identified the PTEN gene as a target of miRNA-221/-222. Furthermore, we found that knocking down miRNA-221/-222 by antisense oligonucleotides upregulated PTEN expression. Upregulated PTEN expression suppressed AKT activity and increased radiation-induced apoptosis, resulting in enhancement of radiosensitivity in tumor cells. Conclusions: miRNA-221/-222 control radiation sensitivity by regulating the PTEN/AKT pathway and can be explored as novel targets for radiosensitization.

  16. Fragment C of Tetanus Toxin: New Insights into Its Neuronal Signaling Pathway

    PubMed Central

    Calvo, Ana C.; Oliván, Sara; Manzano, Raquel; Zaragoza, Pilar; Aguilera, José; Osta, Rosario

    2012-01-01

    When Clostridium tetani was discovered and identified as a Gram-positive anaerobic bacterium of the genus Clostridium, the possibility of turning its toxin into a valuable biological carrier to ameliorate neurodegenerative processes was inconceivable. However, the non-toxic carboxy-terminal fragment of the tetanus toxin heavy chain (fragment C) can be retrogradely transported to the central nervous system; therefore, fragment C has been used as a valuable biological carrier of neurotrophic factors to ameliorate neurodegenerative processes. More recently, the neuroprotective properties of fragment C have also been described in vitro and in vivo, involving the activation of Akt kinase and extracellular signal-regulated kinase (ERK) signaling cascades through neurotrophin tyrosine kinase (Trk) receptors. Although the precise mechanism of the molecular internalization of fragment C in neuronal cells remains unknown, fragment C could be internalized and translocated into the neuronal cytosol through a clathrin-mediated pathway dependent on proteins, such as dynamin and AP-2. In this review, the origins, molecular properties and possible signaling pathways of fragment C are reviewed to understand the biochemical characteristics of its intracellular and synaptic transport. PMID:22837670

  17. Non-repair Pathways for Minimizing Protein Isoaspartyl Damage in the Yeast Saccharomyces cerevisiae*

    PubMed Central

    Patananan, Alexander N.; Capri, Joseph; Whitelegge, Julian P.; Clarke, Steven G.

    2014-01-01

    The spontaneous degradation of asparaginyl and aspartyl residues to isoaspartyl residues is a common type of protein damage in aging organisms. Although the protein-l-isoaspartyl (d-aspartyl) O-methyltransferase (EC 2.1.1.77) can initiate the repair of l-isoaspartyl residues to l-aspartyl residues in most organisms, no gene homolog or enzymatic activity is present in the budding yeast Saccharomyces cerevisiae. Therefore, we used biochemical approaches to elucidate how proteins containing isoaspartyl residues are metabolized in this organism. Surprisingly, the level of isoaspartyl residues in yeast proteins (50–300 pmol of isoaspartyl residues/mg of protein extract) is comparable with organisms with protein-l-isoaspartyl (d-aspartyl) O-methyltransferase, suggesting a novel regulatory pathway. Interfering with common protein quality control mechanisms by mutating and inhibiting the proteasomal and autophagic pathways in vivo did not increase isoaspartyl residue levels compared with wild type or uninhibited cells. However, the inhibition of metalloproteases in in vitro aging experiments by EDTA resulted in an ?3-fold increase in the level of isoaspartyl-containing peptides. Characterization by mass spectrometry of these peptides identified several proteins involved in metabolism as targets of isoaspartyl damage. Further analysis of these peptides revealed that many have an N-terminal isoaspartyl site and originate from proteins with short half-lives. These results suggest that one or more metalloproteases participate in limiting isoaspartyl formation by robust proteolysis. PMID:24764295

  18. A simple separation method for downstream biochemical analysis of aquatic microbes.

    PubMed

    Garrison, Cody E; Bochdansky, Alexander B

    2015-04-01

    In order to study the chemical composition of aquatic microbes it is necessary to obtain completely separated fractions of subpopulations. Size separation by filtration is usually unsuccessful because the smaller group of organisms contaminates the larger fractions due to being trapped on filter surfaces of nominally much larger pore sizes. Here we demonstrate that a simple sucrose density separation method allowed us to separate microorganisms of even subtle size differences and to determine their bulk biochemical composition (proteins, polysaccharides+nucleic acids, and lipids). Both autotrophs and heterotrophs (through anaplerotic pathways) were labeled with (14)C-bicarbonate for biochemical fractionation. We provided proof of concept that eukaryotic microbes could be cleanly separated from prokaryotes in cultures and in field samples, enabling detection of differences in their biochemical makeup. We explored methodological issues regarding separation mechanisms, fixation, and pre-concentration via tangential flow filtration of oligotrophic marine waters where abundances of microorganisms are comparably low. By selecting an appropriate centrifugal force, two processes (i.e., isopycnal and rate-zonal separation) can be exploited simultaneously resulting in finely-separated density fractions, which also resulted in size separation. Future applications of this method include exploration of the stoichiometric, biochemical and genetic differences among subpopulations of microbes in a wide variety of aquatic environments. PMID:25655777

  19. Service-based analysis of biological pathways

    PubMed Central

    Zheng, George; Bouguettaya, Athman

    2009-01-01

    Background Computer-based pathway discovery is concerned with two important objectives: pathway identification and analysis. Conventional mining and modeling approaches aimed at pathway discovery are often effective at achieving either objective, but not both. Such limitations can be effectively tackled leveraging a Web service-based modeling and mining approach. Results Inspired by molecular recognitions and drug discovery processes, we developed a Web service mining tool, named PathExplorer, to discover potentially interesting biological pathways linking service models of biological processes. The tool uses an innovative approach to identify useful pathways based on graph-based hints and service-based simulation verifying user's hypotheses. Conclusion Web service modeling of biological processes allows the easy access and invocation of these processes on the Web. Web service mining techniques described in this paper enable the discovery of biological pathways linking these process service models. Algorithms presented in this paper for automatically highlighting interesting subgraph within an identified pathway network enable the user to formulate hypothesis, which can be tested out using our simulation algorithm that are also described in this paper. PMID:19796403

  20. JNK functions in the non-canonical Wnt pathway to regulate convergent extension movements in vertebrates

    Microsoft Academic Search

    Hiroaki Yamanaka; Tetsuo Moriguchi; Norihisa Masuyama; Morioh Kusakabe; Hiroshi Hanafusa; Ritsuko Takada; Shinji Takada; Eisuke Nishida

    2002-01-01

    Recent genetic studies in Drosophila identified a novel non-canonical Wnt pathway, the planar cell polarity (PCP) pathway, that signals via JNK to control epithelial cell polarity in Drosophila. Most recently, a pathway regulating convergent extension movements during gastrulation in vertebrate embryos has been shown to be a vertebrate equivalent of the PCP pathway. However, it is not known whether the

  1. Stiffness detection and reduction in discrete stochastic simulation of biochemical systems

    PubMed Central

    Pu, Yang; Watson, Layne T.; Cao, Yang

    2011-01-01

    Typical multiscale biochemical models contain fast-scale and slow-scale reactions, where “fast” reactions fire much more frequently than “slow” ones. This feature often causes stiffness in discrete stochastic simulation methods such as Gillespie’s algorithm and the Tau-Leaping method leading to inefficient simulation. This paper proposes a new strategy to automatically detect stiffness and identify species that cause stiffness for the Tau-Leaping method, as well as two stiffness reduction methods. Numerical results on a stiff decaying dimerization model and a heat shock protein regulation model demonstrate the efficiency and accuracy of the proposed methods for multiscale biochemical systems. PMID:21303090

  2. Bayesian Pathway Analysis of Cancer Microarray Data

    PubMed Central

    Korucuoglu, Melike; Isci, Senol; Ozgur, Arzucan; Otu, Hasan H.

    2014-01-01

    High Throughput Biological Data (HTBD) requires detailed analysis methods and from a life science perspective, these analysis results make most sense when interpreted within the context of biological pathways. Bayesian Networks (BNs) capture both linear and nonlinear interactions and handle stochastic events in a probabilistic framework accounting for noise making them viable candidates for HTBD analysis. We have recently proposed an approach, called Bayesian Pathway Analysis (BPA), for analyzing HTBD using BNs in which known biological pathways are modeled as BNs and pathways that best explain the given HTBD are found. BPA uses the fold change information to obtain an input matrix to score each pathway modeled as a BN. Scoring is achieved using the Bayesian-Dirichlet Equivalent method and significance is assessed by randomization via bootstrapping of the columns of the input matrix. In this study, we improve on the BPA system by optimizing the steps involved in “Data Preprocessing and Discretization”, “Scoring”, “Significance Assessment”, and “Software and Web Application”. We tested the improved system on synthetic data sets and achieved over 98% accuracy in identifying the active pathways. The overall approach was applied on real cancer microarray data sets in order to investigate the pathways that are commonly active in different cancer types. We compared our findings on the real data sets with a relevant approach called the Signaling Pathway Impact Analysis (SPIA). PMID:25036210

  3. Diversifying Carotenoid Biosynthetic Pathways by Directed Evolution

    PubMed Central

    Umeno, Daisuke; Tobias, Alexander V.; Arnold, Frances H.

    2005-01-01

    Microorganisms and plants synthesize a diverse array of natural products, many of which have proven indispensable to human health and well-being. Although many thousands of these have been characterized, the space of possible natural products—those that could be made biosynthetically—remains largely unexplored. For decades, this space has largely been the domain of chemists, who have synthesized scores of natural product analogs and have found many with improved or novel functions. New natural products have also been made in recombinant organisms, via engineered biosynthetic pathways. Recently, methods inspired by natural evolution have begun to be applied to the search for new natural products. These methods force pathways to evolve in convenient laboratory organisms, where the products of new pathways can be identified and characterized in high-throughput screening programs. Carotenoid biosynthetic pathways have served as a convenient experimental system with which to demonstrate these ideas. Researchers have mixed, matched, and mutated carotenoid biosynthetic enzymes and screened libraries of these “evolved” pathways for the emergence of new carotenoid products. This has led to dozens of new pathway products not previously known to be made by the assembled enzymes. These new products include whole families of carotenoids built from backbones not found in nature. This review details the strategies and specific methods that have been employed to generate new carotenoid biosynthetic pathways in the laboratory. The potential application of laboratory evolution to other biosynthetic pathways is also discussed. PMID:15755953

  4. Increased Carotenoid Production by the Food Yeast Candida utilis through Metabolic Engineering of the Isoprenoid Pathway

    Microsoft Academic Search

    HIROSHI SHIMADA; KEIJI KONDO; PAUL D. FRASER; YUTAKA MIURA; TOSHIKO SAITO; NORIHIKO MISAWA

    The yeast Candida utilis does not possess an endogenous biochemical pathway for the synthesis of carote- noids. The central isoprenoid pathway concerned with the synthesis of prenyl lipids is present in C. utilis and active in the biosynthesis of ergosterol. In our previous study, we showed that the introduction of exogenous carotenoid genes, crtE, crtB, and crtI, responsible for the

  5. Biochemical Diagnosis of Coenzyme Q10 Deficiency

    PubMed Central

    Yubero, Delia; Montero, Raquel; Artuch, Rafael; Land, John M.; Heales, Simon J.R.; Hargreaves, Iain P.

    2014-01-01

    Coenzyme Q10 (CoQ10) deficiency appears to have a particularly heterogeneous clinical presentation. However, there appear to be 5 recognisable clinical phenotypes: encephalomyopathy, severe infantile multisystemic disease, nephropathy, cerebellar ataxia, and isolated myopathy. However, although useful, clinical symptoms alone are insufficient for the definitive diagnosis of CoQ10 deficiency which relies upon biochemical assessment of tissue CoQ10 status. In this article, we review the biochemical methods used in the diagnosis of human CoQ10 deficiency and indicate the most appropriate tissues for this evaluation. PMID:25126047

  6. A Verilog Compiler for Biochemical Register Computation

    Microsoft Academic Search

    Adriana Fitzgerald; Adam Shea; Marc D. Riedel

    Abstract—This paper,presents,a,compilation,strategy,for synthesizing biochemical,reactions that perform,sequential arith- metic computation on protein quantities, analogous to register- based,computations,in digital systems. This algorithm,is im- plemented,as a compiler,called VERB (Verilog Elements,for Register-Based Biochemistry). From a Verilog file, VERB gen- erates biochemical,reactions that produce,output,quantities as a function of input quantities, performing operations such as addition, subtraction, and multiplication. Sequential operations are,implemented,by,transferring,quantities,between,protein types, based on a

  7. Conservation of the Salt Overly Sensitive Pathway in Rice1[C][W][OA

    PubMed Central

    Martínez-Atienza, Juliana; Jiang, Xingyu; Garciadeblas, Blanca; Mendoza, Imelda; Zhu, Jian-Kang; Pardo, José M.; Quintero, Francisco J.

    2007-01-01

    The salt tolerance of rice (Oryza sativa) correlates with the ability to exclude Na+ from the shoot and to maintain a low cellular Na+/K+ ratio. We have identified a rice plasma membrane Na+/H+ exchanger that, on the basis of genetic and biochemical criteria, is the functional homolog of the Arabidopsis (Arabidopsis thaliana) salt overly sensitive 1 (SOS1) protein. The rice transporter, denoted by OsSOS1, demonstrated a capacity for Na+/H+ exchange in plasma membrane vesicles of yeast (Saccharomyces cerevisiae) cells and reduced their net cellular Na+ content. The Arabidopsis protein kinase complex SOS2/SOS3, which positively controls the activity of AtSOS1, phosphorylated OsSOS1 and stimulated its activity in vivo and in vitro. Moreover, OsSOS1 suppressed the salt sensitivity of a sos1-1 mutant of Arabidopsis. These results represent the first molecular and biochemical characterization of a Na+ efflux protein from monocots. Putative rice homologs of the Arabidopsis protein kinase SOS2 and its Ca2+-dependent activator SOS3 were identified also. OsCIPK24 and OsCBL4 acted coordinately to activate OsSOS1 in yeast cells and they could be exchanged with their Arabidopsis counterpart to form heterologous protein kinase modules that activated both OsSOS1 and AtSOS1 and suppressed the salt sensitivity of sos2 and sos3 mutants of Arabidopsis. These results demonstrate that the SOS salt tolerance pathway operates in cereals and evidences a high degree of structural conservation among the SOS proteins from dicots and monocots. PMID:17142477

  8. Label-Free Imaging and Biochemical Characterization of Bovine Sperm Cells

    PubMed Central

    Ferrara, Maria Antonietta; Di Caprio, Giuseppe; Managò, Stefano; De Angelis, Annalisa; Sirleto, Luigi; Coppola, Giuseppe; De Luca, Anna Chiara

    2015-01-01

    A full label-free morphological and biochemical characterization is desirable to select spermatozoa during preparation for artificial insemination. In order to study these fundamental parameters, we take advantage of two attractive techniques: digital holography (DH) and Raman spectroscopy (RS). DH presents new opportunities for studying morphological aspect of cells and tissues non-invasively, quantitatively and without the need for staining or tagging, while RS is a very specific technique allowing the biochemical analysis of cellular components with a spatial resolution in the sub-micrometer range. In this paper, morphological and biochemical bovine sperm cell alterations were studied using these techniques. In addition, a complementary DH and RS study was performed to identify X- and Y-chromosome-bearing sperm cells. We demonstrate that the two techniques together are a powerful and highly efficient tool elucidating some important criterions for sperm morphological selection and sex-identification, overcoming many of the limitations associated with existing protocols. PMID:25836358

  9. Structure and biochemical characterization of proliferating cellular nuclear antigen from a parasitic protozoon

    SciTech Connect

    Cardona-Felix, Cesar S.; Lara-Gonzalez, Samuel; Brieba, Luis G. (LNLS)

    2012-02-08

    Proliferating cellular nuclear antigen (PCNA) is a toroidal-shaped protein that is involved in cell-cycle control, DNA replication and DNA repair. Parasitic protozoa are early-diverged eukaryotes that are responsible for neglected diseases. In this work, a PCNA from a parasitic protozoon was identified, cloned and biochemically characterized and its crystal structure was determined. Structural and biochemical studies demonstrate that PCNA from Entamoeba histolytica assembles as a homotrimer that is able to interact with and stimulate the activity of a PCNA-interacting peptide-motif protein from E. histolytica, EhDNAligI. The data indicate a conservation of the biochemical mechanisms of PCNA-mediated interactions between metazoa, yeast and parasitic protozoa.

  10. Detecting Pathway-Based Gene-Gene and Gene-Environment Interactions in Pancreatic Cancer

    PubMed Central

    Duell, Eric J.; Bracci, Paige M.; Moore, Jason H.; Burk, Robert D.; Kelsey, Karl T.; Holly, Elizabeth A.

    2015-01-01

    Data mining and data reduction methods to detect interactions in epidemiologic data are being developed and tested. In these analyses, multifactor dimensionality reduction, focused interaction testing framework, and traditional logistic regression models were used to identify potential interactions with up to three factors. These techniques were used in a population-based case-control study of pancreatic cancer from the San Francisco Bay Area (308 cases, 964 controls). From 7 biochemical pathways, along with tobacco smoking, 26 polymorphisms in 20 genes were included in these analyses. Combinations of genetic markers and cigarette smoking were identified as potential risk factors for pancreatic cancer, including genes in base excision repair (OGG1), nucleotide excision repair (XPD, XPA, XPC), and double-strand break repair (XRCC3). XPD.751, XPD.312, and cigarette smoking were the best single-factor predictors of pancreatic cancer risk, whereas XRCC3.241*smoking and OGG1.326*XPC.PAT were the best two-factor predictors. There was some evidence for a three-factor combination of OGG1.326*XPD.751*smoking, but the covariate-adjusted relative-risk estimates lacked precision. Multifactor dimensionality reduction and focused interaction testing framework showed little concordance, whereas logistic regression allowed for covariate adjustment and model confirmation. Our data suggest that multiple common alleles from DNA repair pathways in combination with cigarette smoking may increase the risk for pancreatic cancer, and that multiple approaches to data screening and analysis are necessary to identify potentially new risk factor combinations. PMID:18559563

  11. Comparative Life Cycle Assessment of Lignocellulosic Ethanol Production: Biochemical Versus Thermochemical Conversion

    NASA Astrophysics Data System (ADS)

    Mu, Dongyan; Seager, Thomas; Rao, P. Suresh; Zhao, Fu

    2010-10-01

    Lignocellulosic biomass can be converted into ethanol through either biochemical or thermochemical conversion processes. Biochemical conversion involves hydrolysis and fermentation while thermochemical conversion involves gasification and catalytic synthesis. Even though these routes produce comparable amounts of ethanol and have similar energy efficiency at the plant level, little is known about their relative environmental performance from a life cycle perspective. Especially, the indirect impacts, i.e. emissions and resource consumption associated with the production of various process inputs, are largely neglected in previous studies. This article compiles material and energy flow data from process simulation models to develop life cycle inventory and compares the fossil fuel consumption, greenhouse gas emissions, and water consumption of both biomass-to-ethanol production processes. The results are presented in terms of contributions from feedstock, direct, indirect, and co-product credits for four representative biomass feedstocks i.e., wood chips, corn stover, waste paper, and wheat straw. To explore the potentials of the two conversion pathways, different technological scenarios are modeled, including current, 2012 and 2020 technology targets, as well as different production/co-production configurations. The modeling results suggest that biochemical conversion has slightly better performance on greenhouse gas emission and fossil fuel consumption, but that thermochemical conversion has significantly less direct, indirect, and life cycle water consumption. Also, if the thermochemical plant operates as a biorefinery with mixed alcohol co-products separated for chemicals, it has the potential to achieve better performance than biochemical pathway across all environmental impact categories considered due to higher co-product credits associated with chemicals being displaced. The results from this work serve as a starting point for developing full life cycle assessment model that facilitates effective decision-making regarding lignocellulosic ethanol production.

  12. Reduced-order modelling of biochemical networks: application to the GTPase-cycle signalling module

    PubMed Central

    Maurya, M.R.; Bornheimer, S.J.; Venkatasubramanian, V.; Subramaniam, S.

    2011-01-01

    Biochemical systems embed complex networks and hence development and analysis of their detailed models pose a challenge for computation. Coarse-grained biochemical models, called reduced-order models (ROMs), consisting of essential biochemical mechanisms are more useful for computational analysis and for studying important features of a biochemical network. The authors present a novel method to model-reduction by identifying potentially important parameters using multidimensional sensitivity analysis. A ROM is generated for the GTPase-cycle module of m1 muscarinic acetylcholine receptor, Gq, and regulator of G-protein signalling 4 (a GTPase-activating protein or GAP) starting from a detailed model of 48 reactions. The resulting ROM has only 17 reactions. The ROM suggested that complexes of G-protein coupled receptor (GPCR) and GAP – which were proposed in the detailed model as a hypothesis – are required to fit the experimental data. Models previously published in the literature are also simulated and compared with the ROM. Through this comparison, a minimal ROM, that also requires complexes of GPCR and GAP, with just 15 parameters is generated. The proposed reduced-order modelling methodology is scalable to larger networks and provides a general framework for the reduction of models of biochemical systems. PMID:16986265

  13. Looking beneath the surface: the cell death pathway of Fas/APO-1 (CD95).

    PubMed Central

    Stanger, B. Z.

    1996-01-01

    SUMMARY: The biochemical basis of programmed cell death is poorly understood in mammals. The cell surface receptor Fas/APO-1 (CD95) is one molecule known to be central to a number of mammalian cell death processes. Several studies in the past year have led to insights about the role of Fas/APO-1 in vivo and have also given some clues about the biochemical components of the Fas/APO-1 death pathway. This article reviews those studies and discuss models of Fas/APO-1 signaling and function. BACKGROUND: Cell death occurs as a normal process in a wide variety of developmental and homeostatic contexts in metazoan organisms (1); it represents the timely and appropriate fate for many or even the majority of cells born in certain organ systems. Despite the importance and ubiquitous nature of such physiologic, or "programmed", cell death, little is known about the molecular events that mediate this process. That a conserved biochemical pathway exists is suggested by the observation that programmed cell death is almost always accompanied by a consistent set of morphologic changes, an appearance known as apoptosis (2). The identification of the genes that control programmed cell death in higher eukaryotes has been hampered by several inherent difficulties. First, the genetic tools so useful in dissecting cell death pathways in Caenorhabditis elegans (3) and Drosophila (4) have not been available in higher eukaryotes. Second, the death-inducing properties of such genes makes genetic selection an impractical means of identification. Third, it appears that many cell death genes are constitutively expressed and present in an inactive form (5), making it unlikely that they could be discovered by techniques relying upon differential gene expression. Finally, genes identified by virtue of an ability to induce death when overexpressed must be subjected to rigorous criteria to determine whether the cell death is of physiologic importance, since it is likely that overexpression of certain proteins may lead to toxic effects that are distinct from the in vivo roles of those proteins. Two approaches to date have yielded the most information about cell death processes: (i) identification of cell death genes by classical genetic means coupled with characterization of their mammalian homologs and (ii) screening for proteins capable of inducing cell death directly in mammalian cells. The Fas antigen/APO-1 is an example of a protein discovered using the latter approach, as it was first discovered as an inducer of cell death and later shown to be necessary and sufficient for certain programmed deaths in vivo. More recent studies have connected Fas to elements of cell death pathways in other species. It has been proposed that Fas is related to the Drosophila cell death protein Reaper, and that in signaling cell death Fas relies upon a relative of the C. elegans cell death protein CED-3. Fas may therefore represent an evolutionarily conserved component of a universal cell death pathway. Images FIG. 1 PMID:8900530

  14. Formaldehyde-detoxifying role of the tetrahydromethanopterin-linked pathway in Methylobacterium extorquens AM1.

    PubMed

    Marx, Christopher J; Chistoserdova, Ludmila; Lidstrom, Mary E

    2003-12-01

    The facultative methylotroph Methylobacterium extorquens AM1 possesses two pterin-dependent pathways for C(1) transfer between formaldehyde and formate, the tetrahydrofolate (H(4)F)-linked pathway and the tetrahydromethanopterin (H(4)MPT)-linked pathway. Both pathways are required for growth on C(1) substrates; however, mutants defective for the H(4)MPT pathway reveal a unique phenotype of being inhibited by methanol during growth on multicarbon compounds such as succinate. It has been previously proposed that this methanol-sensitive phenotype is due to the inability to effectively detoxify formaldehyde produced from methanol. Here we present a comparative physiological characterization of four mutants defective in the H(4)MPT pathway and place them into three different phenotypic classes that are concordant with the biochemical roles of the respective enzymes. We demonstrate that the analogous H(4)F pathway present in M. extorquens AM1 cannot fulfill the formaldehyde detoxification function, while a heterologously expressed pathway linked to glutathione and NAD(+) can successfully substitute for the H(4)MPT pathway. Additionally, null mutants were generated in genes previously thought to be essential, indicating that the H(4)MPT pathway is not absolutely required during growth on multicarbon compounds. These results define the role of the H(4)MPT pathway as the primary formaldehyde oxidation and detoxification pathway in M. extorquens AM1. PMID:14645276

  15. Comparison of transcripts in Phalaenopsis bellina and Phalaenopsis equestris (Orchidaceae) flowers to deduce monoterpene biosynthesis pathway

    PubMed Central

    Hsiao, Yu-Yun; Tsai, Wen-Chieh; Kuoh, Chang-Sheng; Huang, Tian-Hsiang; Wang, Hei-Chia; Wu, Tian-Shung; Leu, Yann-Lii; Chen, Wen-Huei; Chen, Hong-Hwa

    2006-01-01

    Background Floral scent is one of the important strategies for ensuring fertilization and for determining seed or fruit set. Research on plant scents has hampered mainly by the invisibility of this character, its dynamic nature, and complex mixtures of components that are present in very small quantities. Most progress in scent research, as in other areas of plant biology, has come from the use of molecular and biochemical techniques. Although volatile components have been identified in several orchid species, the biosynthetic pathways of orchid flower fragrance are far from understood. We investigated how flower fragrance was generated in certain Phalaenopsis orchids by determining the chemical components of the floral scent, identifying floral expressed-sequence-tags (ESTs), and deducing the pathways of floral scent biosynthesis in Phalaneopsis bellina by bioinformatics analysis. Results The main chemical components in the P. bellina flower were shown by gas chromatography-mass spectrometry to be monoterpenoids, benzenoids and phenylpropanoids. The set of floral scent producing enzymes in the biosynthetic pathway from glyceraldehyde-3-phosphate (G3P) to geraniol and linalool were recognized through data mining of the P. bellina floral EST database (dbEST). Transcripts preferentially expressed in P. bellina were distinguished by comparing the scent floral dbEST to that of a scentless species, P. equestris, and included those encoding lipoxygenase, epimerase, diacylglycerol kinase and geranyl diphosphate synthase. In addition, EST filtering results showed that transcripts encoding signal transduction and Myb transcription factors and methyltransferase, in addition to those for scent biosynthesis, were detected by in silico hybridization of the P. bellina unigene database against those of the scentless species, rice and Arabidopsis. Altogether, we pinpointed 66% of the biosynthetic steps from G3P to geraniol, linalool and their derivatives. Conclusion This systems biology program combined chemical analysis, genomics and bioinformatics to elucidate the scent biosynthesis pathway and identify the relevant genes. It integrates the forward and reverse genetic approaches to knowledge discovery by which researchers can study non-model plants. PMID:16836766

  16. Biochemical Approaches to Improved Nitrogen Fixation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Improving symbiotic nitrogen fixation by legumes has emerged again as an important topic on the world scene due to the energy crisis and lack of access to nitrogen fertilizer in developing countries. We have taken a biochemical genomics approach to improving symbiotic nitrogen fixation in legumes. L...

  17. Congenital adrenal hyperplasia: biochemical and molecular perspectives.

    PubMed

    Maitra, Anurupa; Shirwalkar, Heena

    2003-07-01

    Congenital adrenal hyperplasia is a disorder occurring in both sexes and is the commonest cause of ambiguous genitalia. It is a group of autosomal recessive disorders in which, on the basis of an enzyme defect the bulk of steroid hormone production by adrenal cortex shifts from corticosteroids to androgens. Autosomal recessive mutations in the CYP21, CYP17, CYP11B1 and 3betaHSD genes that encode steroidogenic enzymes, in addition to mutations in the gene encoding the intracellular cholesterol transport protein steroidogenic acute regulatory protein StAR can cause CAH. Each of the defects causes different biochemical consequences and clinical features. Deficiencies in 21 hydroxylase (21-OH) and 11beta-Hydroxylase (11beta-OH) are the two most frequent causes of CAH. All the biochemical defects impair cortisol secretion, resulting into compensatory hypersecretion of ACTH and consequent hyperplasia of the adrenal cortex. Research in recent years has clarified clinical, biochemical and genetic problems in diagnosis and treatment of the disorders. Expanding knowledge of the gene mutations associated with each of these disorders is providing valuable diagnostic tools in addition to the biochemical profile and phenotype. Genotyping is useful in selecting instances to provide genetic counseling and to clarify ambiguous cases. PMID:15255373

  18. The biochemical properties of the pulmonary circulation

    Microsoft Academic Search

    J. A. Pang; D. M. Geddes

    1981-01-01

    The biochemical properties of the pulmonary circulation are reviewed, with special reference to the fate of biologically active\\u000a substances in the blood. Possible physiological, pathological, pharmacological and practical implications of clinical relevance\\u000a are discussed.

  19. Quantifying robustness of biochemical network models

    Microsoft Academic Search

    Lan Ma; Pablo A. Iglesias

    2002-01-01

    Background: Robustness of mathematical models of biochemical networks is important for validation purposes and can be used as a means of selecting between different competing models. Tools for quantifying parametric robustness are needed. Results: Two techniques for describing quantitatively the robustness of an oscillatory model were presented and contrasted. Single-parameter bifurcation analysis was used to evaluate the stability robustness of

  20. Potential biochemical therapy of glioma cancer

    Microsoft Academic Search

    Li-Tian Yin; Yue-Jun Fu; Qiao-Ling Xu; Jun Yang; Zeng-Li Liu; Ai-Hua Liang; Xiao-Jun Fan; Cheng-Gang Xu

    2007-01-01

    Glioma is a highly invasive, rapidly spreading form of brain cancer that is resistant to surgical and medical treatment. The recent progresses made in intracellular and ion channels of glioma cells provide a potential new approach for biochemical therapy of brain tumor. In this paper, we reviewed clinical data on chemotherapy by temozolomide and results from new studies on voltage-gated

  1. CMOS Microsystems for Phase Fluorometric Biochemical Monitoring

    Microsoft Academic Search

    Alexander N. Cartwright; Vamsy P. Chodavarapu; Sung Jin Kim; Rachel M. Bukowski; Albert H. Titus; Frank V. Bright

    2007-01-01

    This article will present a review of our recent work on the development of Complementary Metal-Oxide Semiconductor (CMOS) detection and signal processing interfaces for fluorescence based biochemical sensors as well as the development of a new sensor. We will discuss a number of microsystems that integrate CMOS Application Specific Integrated Circuits (ASICs) with nanoporous sensor materials. Specifically, sol-gel derived xerogel

  2. Computing Resources at Chemical and Biochemical Engineering

    E-print Network

    Computing Resources at Chemical and Biochemical Engineering Note that use of all Rutgers University computer systems is subject to the Rutgers University Computing Services' Acceptable Use Policy, viewable undergraduates. To obtain a departmental Windows NT user account, see Getting and using computer accounts

  3. Biochemical and genetic studies on mammalian cells

    Microsoft Academic Search

    Theodore T. Puck

    1971-01-01

    A methodology is developed for the investigation of biochemical and ; genetic phenomena associated with mammalian cell cultures. During the course of ; the discussion, the mutagenic effects of EMS, X rays, and ultraviolet radiation ; are mentioned. The modifying effects of caffeine on the survival curves of x- ; and ultraviolet irradiated mammalian cells is also discussed. (ERB);

  4. Biochemical characterization of the antioxidant system in the scallop Adamussium colbecki, a sentinel organism for monitoring the Antarctic environment

    Microsoft Academic Search

    F. Regoli; G. B. Principato; E. Bertoli; M. Nigro; E. Orlando

    1997-01-01

    The scallop Adamussium colbecki can be profitably used for monitoring Antarctic coastal environments but its utility would be increased if chemical analyses\\u000a of pollutants were integrated with data on their biological effects. Since oxidative stress is a common pathway of toxicity\\u000a induced by xenobiotics, a preliminary biochemical characterization was carried out on the antioxidant system of this species\\u000a and baseline

  5. Multiplex Analysis of Intracellular Signaling Pathways in Lymphoid Cells by Microbead Suspension Arrays

    Microsoft Academic Search

    Imran H. Khan; Sara Mendoza; Paul Rhyne; Melanie Ziman; Joseph Tuscano; Dominic Eisinger; Hsing-Jien Kung; Paul A. Luciw

    2005-01-01

    Phosphorylation analysis of signaling proteins is key for examining intracellular signaling pathways. Conventional biochemical approaches, e.g. immunoprecipitation, West- ern blot, and ELISA, have played a major role in elucida- tion of individual signaling events. However, these meth- ods are laborious, time-consuming, and difficult to adapt for high throughput analysis. A multiplex approach to measure phosphorylation state of multiple signaling pro-