G-NEST: A gene neighborhood scoring tool to identify co-conserved, co-expressed genes

Science.gov (United States)

In previous studies, gene neighborhoods--spatial clusters of co-expressed genes in the genome--have been defined using arbitrary rules such as requiring adjacency, a minimum number of genes, a fixed window size, or a minimum expression level. In the current study, we developed a Gene Neighborhood Sc...

G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes

Directory of Open Access Journals (Sweden)

Lemay Danielle G

2012-09-01

Full Text Available Abstract Background In previous studies, gene neighborhoods—spatial clusters of co-expressed genes in the genome—have been defined using arbitrary rules such as requiring adjacency, a minimum number of genes, a fixed window size, or a minimum expression level. In the current study, we developed a Gene Neighborhood Scoring Tool (G-NEST which combines genomic location, gene expression, and evolutionary sequence conservation data to score putative gene neighborhoods across all possible window sizes simultaneously. Results Using G-NEST on atlases of mouse and human tissue expression data, we found that large neighborhoods of ten or more genes are extremely rare in mammalian genomes. When they do occur, neighborhoods are typically composed of families of related genes. Both the highest scoring and the largest neighborhoods in mammalian genomes are formed by tandem gene duplication. Mammalian gene neighborhoods contain highly and variably expressed genes. Co-localized noisy gene pairs exhibit lower evolutionary conservation of their adjacent genome locations, suggesting that their shared transcriptional background may be disadvantageous. Genes that are essential to mammalian survival and reproduction are less likely to occur in neighborhoods, although neighborhoods are enriched with genes that function in mitosis. We also found that gene orientation and protein-protein interactions are partially responsible for maintenance of gene neighborhoods. Conclusions Our experiments using G-NEST confirm that tandem gene duplication is the primary driver of non-random gene order in mammalian genomes. Non-essentiality, co-functionality, gene orientation, and protein-protein interactions are additional forces that maintain gene neighborhoods, especially those formed by tandem duplicates. We expect G-NEST to be useful for other applications such as the identification of core regulatory modules, common transcriptional backgrounds, and chromatin domains. The

Large clusters of co-expressed genes in the Drosophila genome.

Science.gov (United States)

Boutanaev, Alexander M; Kalmykova, Alla I; Shevelyov, Yuri Y; Nurminsky, Dmitry I

2002-12-12

Clustering of co-expressed, non-homologous genes on chromosomes implies their co-regulation. In lower eukaryotes, co-expressed genes are often found in pairs. Clustering of genes that share aspects of transcriptional regulation has also been reported in higher eukaryotes. To advance our understanding of the mode of coordinated gene regulation in multicellular organisms, we performed a genome-wide analysis of the chromosomal distribution of co-expressed genes in Drosophila. We identified a total of 1,661 testes-specific genes, one-third of which are clustered on chromosomes. The number of clusters of three or more genes is much higher than expected by chance. We observed a similar trend for genes upregulated in the embryo and in the adult head, although the expression pattern of individual genes cannot be predicted on the basis of chromosomal position alone. Our data suggest that the prevalent mechanism of transcriptional co-regulation in higher eukaryotes operates with extensive chromatin domains that comprise multiple genes.

Co-Expression of Neighboring Genes in the Zebrafish (Danio rerio Genome

Directory of Open Access Journals (Sweden)

Daryi Wang

2009-08-01

Full Text Available Neighboring genes in the eukaryotic genome have a tendency to express concurrently, and the proximity of two adjacent genes is often considered a possible explanation for their co-expression behavior. However, the actual contribution of the physical distance between two genes to their co-expression behavior has yet to be defined. To further investigate this issue, we studied the co-expression of neighboring genes in zebrafish, which has a compact genome and has experienced a whole genome duplication event. Our analysis shows that the proportion of highly co-expressed neighboring pairs (Pearson’s correlation coefficient R>0.7 is low (0.24% ~ 0.67%; however, it is still significantly higher than that of random pairs. In particular, the statistical result implies that the co-expression tendency of neighboring pairs is negatively correlated with their physical distance. Our findings therefore suggest that physical distance may play an important role in the co-expression of neighboring genes. Possible mechanisms related to the neighboring genes’ co-expression are also discussed.

Open Method of Co-Ordination for Demoi-Cracy?

DEFF Research Database (Denmark)

Borrás, Susana; Radaelli, Claudio

2014-01-01

Under which conditions does the open method of co-ordination match the standards for demoi-cracy? To answer this question, we need some explicit standards about demoi-cracy. In fact, open co-ordination serves three different but interrelated purposes in European Union policy: to facilitate...... convergence; to support learning processes; and to encourage exploration of policy innovation. By intersecting standards and purposes, we find open co-ordination is neither inherently ‘good’ nor ‘bad’ for demoi-cracy, as it depends on how it has been put into practice. Therefore, we qualify the answer...

Lanthanide co-ordination frameworks: Opportunities and diversity

International Nuclear Information System (INIS)

Hill, Robert J.; Long, De-Liang; Hubberstey, Peter; Schroeder, Martin; Champness, Neil R.

2005-01-01

Significant successes have been made over recent years in preparing co-ordination framework polymers that show macroscopic material properties, but in the vast majority of cases this has been achieved with d-block metal-based systems. Lanthanide co-ordination frameworks also offer attractive properties in terms of their potential applications as luminescent, non-linear optical and porous materials. However, lanthanide-based systems have been far less studied to date than their d-block counterparts. One possible reason for this is that the co-ordination spheres of lanthanide cations are more difficult to control and, in the absence of design strategies for lanthanide co-ordination frameworks, it is significantly more difficult to target materials with specific properties. However, this article highlights some of the exciting possibilities that have emerged from the earliest investigations in this field with new topological families of compounds being discovered from relatively simple framework components, including unusual eight, seven and five-connected framework systems. Our own research, as well as others, is leading to a much greater appreciation of the factors that control framework formation and the resultant observed topologies of these polymers. As this understanding develops targeting particular framework types will become more straightforward and the development of designed polyfunctional materials more accessible. Thus, it can be seen that lanthanide co-ordination frameworks have the potential to open up previously unexplored directions for materials chemistry. This article focuses on the underlying concepts for the construction of these enticing and potentially highly important materials

Co-ordinated action between youth-care and sports: facilitators and barriers.

Science.gov (United States)

Hermens, Niels; de Langen, Lisanne; Verkooijen, Kirsten T; Koelen, Maria A

2017-07-01

In the Netherlands, youth-care organisations and community sports clubs are collaborating to increase socially vulnerable youths' participation in sport. This is rooted in the idea that sports clubs are settings for youth development. As not much is known about co-ordinated action involving professional care organisations and community sports clubs, this study aims to generate insight into facilitators of and barriers to successful co-ordinated action between these two organisations. A cross-sectional study was conducted using in-depth semi-structured qualitative interview data. In total, 23 interviews were held at five locations where co-ordinated action between youth-care and sports takes place. Interviewees were youth-care workers, representatives from community sports clubs, and Care Sport Connectors who were assigned to encourage and manage the co-ordinated action. Using inductive coding procedures, this study shows that existing and good relationships, a boundary spanner, care workers' attitudes, knowledge and competences of the participants, organisational policies and ambitions, and some elements external to the co-ordinated action were reported to be facilitators or barriers. In addition, the participants reported that the different facilitators and barriers influenced the success of the co-ordinated action at different stages of the co-ordinated action. Future research is recommended to further explore the role of boundary spanners in co-ordinated action involving social care organisations and community sports clubs, and to identify what external elements (e.g. events, processes, national policies) are turning points in the formation, implementation and continuation of such co-ordinated action. © 2017 John Wiley & Sons Ltd.

Anatomical localization of electrophysiological recording sites by co-ordinate transformation.

Science.gov (United States)

Sinex, D G

1997-07-18

A method for estimating the anatomical locations of the units recorded in electrophysiological mapping experiments is described. A total of three locations must be marked by dye injections or electrolytic lesions and identified in tissue sections. From those locations, equations are derived to translate, scale, and rotate the three-dimensional co-ordinates of the recording sites, so that they are correct for a second, three-dimensional co-ordinate system based on the anatomy of the mapped structure. There is no limit to the number of recording sites that can be localized. This differs from methods that require a dye injection or lesion to be made at the exact location at which a particular unit was recorded. The accuracy of the transformed co-ordinates is limited by the accuracy with which the co-ordinates can be measured: in test measurements and in the experiments for which this algorithm was developed, the computed co-ordinates were typically accurate to within 100 microns or less.

The Design Co-ordination Framework: key elements for effective product development

DEFF Research Database (Denmark)

Andreasen, Mogens Myrup; Bowen, J.; Storm, T.

1997-01-01

This paper proposes a Design Co-ordination Framework (DCF) i.e. a concept for an ideal DC system with the abilities to support co-ordination of various complex aspects of product development. A set of frames, modelling key elements of co-ordination, which reflect the states of design, plans, orga...

Using GIS to check co-ordinates of genebank accessions

NARCIS (Netherlands)

Hijmans, R.J.; Schreuder, M.; Cruz, de la J.; Guarino, L.

1999-01-01

The geographic co-ordinates of the locations where germplasm accessions have been collected are usually documented in genebank databases. However, the co-ordinate data are often incomplete and may contain errors. This paper describes procedures to check for errors, to determine the cause of these

Co-ordination Action on Ocean Energy (CA-OE)

DEFF Research Database (Denmark)

Tedd, James; Frigaard, Peter

In October 2004, the Co-ordination Action on Ocean Energy (CA-OE) was launched, co-financed by the European Commission, under the Renewable Energy Technologies priority within the 6th Framework programme, contract number 502701, chaired by Kim Nielsen, Rambøll, Denmark. The project involves 41...... partners. In general the public is not aware of the development of ocean energy and its exploitation. There is a need to make a united effort from the developers and research community to present the various principles and results in a coordinated manner with public appeal. The main objectives of the Co......-ordination Action on Ocean Energy are: To develop a common knowledge base necessary for coherent research and development policiesTo bring a co-ordinated approach within key areas of ocean energy research and development.To provide a forum for the longer term marketing of promising research developments...

2D co-ordinate transformation based on a spike timing-dependent plasticity learning mechanism.

Science.gov (United States)

Wu, QingXiang; McGinnity, Thomas Martin; Maguire, Liam; Belatreche, Ammar; Glackin, Brendan

2008-11-01

In order to plan accurate motor actions, the brain needs to build an integrated spatial representation associated with visual stimuli and haptic stimuli. Since visual stimuli are represented in retina-centered co-ordinates and haptic stimuli are represented in body-centered co-ordinates, co-ordinate transformations must occur between the retina-centered co-ordinates and body-centered co-ordinates. A spiking neural network (SNN) model, which is trained with spike-timing-dependent-plasticity (STDP), is proposed to perform a 2D co-ordinate transformation of the polar representation of an arm position to a Cartesian representation, to create a virtual image map of a haptic input. Through the visual pathway, a position signal corresponding to the haptic input is used to train the SNN with STDP synapses such that after learning the SNN can perform the co-ordinate transformation to generate a representation of the haptic input with the same co-ordinates as a visual image. The model can be applied to explain co-ordinate transformation in spiking neuron based systems. The principle can be used in artificial intelligent systems to process complex co-ordinate transformations represented by biological stimuli.

Metal selective co-ordinative self-assembly of π-donors

Indian Academy of Sciences (India)

Metal selective co-ordinative nanostructures were constructed by the supramolecular ... observed an anomalous binding of metal ion to the core sulphur groups causing redox changes in the TTF ... attention on metal-assisted co-ordinative self-assembly ..... M TTF-Py in 1:1 CHCl3: MeCN and (c) photographs showing visual.

Co-expression network analysis of duplicate genes in maize (Zea mays L.) reveals no subgenome bias.

Science.gov (United States)

Li, Lin; Briskine, Roman; Schaefer, Robert; Schnable, Patrick S; Myers, Chad L; Flagel, Lex E; Springer, Nathan M; Muehlbauer, Gary J

2016-11-04

Gene duplication is prevalent in many species and can result in coding and regulatory divergence. Gene duplications can be classified as whole genome duplication (WGD), tandem and inserted (non-syntenic). In maize, WGD resulted in the subgenomes maize1 and maize2, of which maize1 is considered the dominant subgenome. However, the landscape of co-expression network divergence of duplicate genes in maize is still largely uncharacterized. To address the consequence of gene duplication on co-expression network divergence, we developed a gene co-expression network from RNA-seq data derived from 64 different tissues/stages of the maize reference inbred-B73. WGD, tandem and inserted gene duplications exhibited distinct regulatory divergence. Inserted duplicate genes were more likely to be singletons in the co-expression networks, while WGD duplicate genes were likely to be co-expressed with other genes. Tandem duplicate genes were enriched in the co-expression pattern where co-expressed genes were nearly identical for the duplicates in the network. Older gene duplications exhibit more extensive co-expression variation than younger duplications. Overall, non-syntenic genes primarily from inserted duplications show more co-expression divergence. Also, such enlarged co-expression divergence is significantly related to duplication age. Moreover, subgenome dominance was not observed in the co-expression networks - maize1 and maize2 exhibit similar levels of intra subgenome correlations. Intriguingly, the level of inter subgenome co-expression was similar to the level of intra subgenome correlations, and genes from specific subgenomes were not likely to be the enriched in co-expression network modules and the hub genes were not predominantly from any specific subgenomes in maize. Our work provides a comprehensive analysis of maize co-expression network divergence for three different types of gene duplications and identifies potential relationships between duplication types

Co-ordination of heterovalent cation impurities in molten salts

International Nuclear Information System (INIS)

Andreoni, W.; Rovere, M.; Tosi, M.P.

1982-01-01

The local liquid structure around heterovalent cation impurities in molten chlorides is discussed in relation to spectroscopic data on solutions of transition metal ions. A tightly packed, low co-ordination shell is shown to be favoured by Coulomb ionic interactions for physically reasonable values of the size of the impurity. A competition between these forces and ''crystal field'' interactions favouring octahedral co-ordination is thus to be expected for many transition metal ions, as suggested by Gruen and McBeth. The transition observed for some transition metal ions from higher to lower co-ordination with increasing temperature is attributed primarily to entropy differences, that are roughly estimated in a solid-like model. (author)

Characterization of chemically induced liver injuries using gene co-expression modules.

Directory of Open Access Journals (Sweden)

Gregory J Tawa

Full Text Available Liver injuries due to ingestion or exposure to chemicals and industrial toxicants pose a serious health risk that may be hard to assess due to a lack of non-invasive diagnostic tests. Mapping chemical injuries to organ-specific damage and clinical outcomes via biomarkers or biomarker panels will provide the foundation for highly specific and robust diagnostic tests. Here, we have used DrugMatrix, a toxicogenomics database containing organ-specific gene expression data matched to dose-dependent chemical exposures and adverse clinical pathology assessments in Sprague Dawley rats, to identify groups of co-expressed genes (modules specific to injury endpoints in the liver. We identified 78 such gene co-expression modules associated with 25 diverse injury endpoints categorized from clinical pathology, organ weight changes, and histopathology. Using gene expression data associated with an injury condition, we showed that these modules exhibited different patterns of activation characteristic of each injury. We further showed that specific module genes mapped to 1 known biochemical pathways associated with liver injuries and 2 clinically used diagnostic tests for liver fibrosis. As such, the gene modules have characteristics of both generalized and specific toxic response pathways. Using these results, we proposed three gene signature sets characteristic of liver fibrosis, steatosis, and general liver injury based on genes from the co-expression modules. Out of all 92 identified genes, 18 (20% genes have well-documented relationships with liver disease, whereas the rest are novel and have not previously been associated with liver disease. In conclusion, identifying gene co-expression modules associated with chemically induced liver injuries aids in generating testable hypotheses and has the potential to identify putative biomarkers of adverse health effects.

Elucidating gene function and function evolution through comparison of co-expression networks in plants

Directory of Open Access Journals (Sweden)

Marek eMutwil

2014-08-01

Full Text Available The analysis of gene expression data has shown that transcriptionally coordinated (co-expressed genes are often functionally related, enabling scientists to use expression data in gene function prediction. This Focused Review discusses our original paper (Large-scale co-expression approach to dissect secondary cell wall formation across plant species, Frontiers in Plant Science 2:23. In this paper we applied cross-species analysis to co-expression networks of genes involved in cellulose biosynthesis. We show that the co-expression networks from different species are highly similar, indicating that whole biological pathways are conserved across species. This finding has two important implications. First, the analysis can transfer gene function annotation from well-studied plants, such as Arabidopsis, to other, uncharacterized plant species. As the analysis finds genes that have similar sequence and similar expression pattern across different organisms, functionally equivalent genes can be identified. Second, since co-expression analyses are often noisy, a comparative analysis should have higher performance, as parts of co-expression networks that are conserved are more likely to be functionally relevant. In this Focused Review, we outline the comparative analysis done in the original paper and comment on the recent advances and approaches that allow comparative analyses of co-function networks. We hypothesize that, in comparison to simple co-expression analysis, comparative analysis would yield more accurate gene function predictions. Finally, by combining comparative analysis with genomic information of green plants, we propose a possible composition of cellulose biosynthesis machinery during earlier stages of plant evolution.

The Arabidopsis co-expression tool (act): a WWW-based tool and database for microarray-based gene expression analysis

DEFF Research Database (Denmark)

Jen, C. H.; Manfield, I. W.; Michalopoulos, D. W.

2006-01-01

be examined using the novel clique finder tool to determine the sets of genes most likely to be regulated in a similar manner. In combination, these tools offer three levels of analysis: creation of correlation lists of co-expressed genes, refinement of these lists using two-dimensional scatter plots......We present a new WWW-based tool for plant gene analysis, the Arabidopsis Co-Expression Tool (act) , based on a large Arabidopsis thaliana microarray data set obtained from the Nottingham Arabidopsis Stock Centre. The co-expression analysis tool allows users to identify genes whose expression...

Normal co-ordinate analysis of 1, 8-dibromooctane

Science.gov (United States)

Singh, Devinder; Jaggi, Neena; Singh, Nafa

2010-02-01

The organic compound 1,8-dibromooctane (1,8-DBO) exists in liquid phase at ambient temperatures and has versatile synthetic applications. In its liquid phase 1,8-DBO has been expected to exist in four most probable conformations, with all its carbon atoms in the same plane, having symmetries C 2h , C i , C 2 and C 1 . In the present study a detailed vibrational analysis in terms of assignment of Fourier transform infrared (FT-IR) and Raman bands of this molecule using normal co-ordinate calculations has been done. A systematic set of symmetry co-ordinates has been constructed for this molecule and normal co-ordinate analysis is carried out using the computer program MOLVIB. The force-field transferred from already studied lower chain bromo-alkanes is subjected to refinement so as to fit the observed infrared and Raman frequencies with those of calculated ones. The potential energy distribution (PED) has also been calculated for each mode of vibration of the molecule for the assumed conformations.

VTCdb: a gene co-expression database for the crop species Vitis vinifera (grapevine).

Science.gov (United States)

Wong, Darren C J; Sweetman, Crystal; Drew, Damian P; Ford, Christopher M

2013-12-16

Gene expression datasets in model plants such as Arabidopsis have contributed to our understanding of gene function and how a single underlying biological process can be governed by a diverse network of genes. The accumulation of publicly available microarray data encompassing a wide range of biological and environmental conditions has enabled the development of additional capabilities including gene co-expression analysis (GCA). GCA is based on the understanding that genes encoding proteins involved in similar and/or related biological processes may exhibit comparable expression patterns over a range of experimental conditions, developmental stages and tissues. We present an open access database for the investigation of gene co-expression networks within the cultivated grapevine, Vitis vinifera. The new gene co-expression database, VTCdb (http://vtcdb.adelaide.edu.au/Home.aspx), offers an online platform for transcriptional regulatory inference in the cultivated grapevine. Using condition-independent and condition-dependent approaches, grapevine co-expression networks were constructed using the latest publicly available microarray datasets from diverse experimental series, utilising the Affymetrix Vitis vinifera GeneChip (16 K) and the NimbleGen Grape Whole-genome microarray chip (29 K), thus making it possible to profile approximately 29,000 genes (95% of the predicted grapevine transcriptome). Applications available with the online platform include the use of gene names, probesets, modules or biological processes to query the co-expression networks, with the option to choose between Affymetrix or Nimblegen datasets and between multiple co-expression measures. Alternatively, the user can browse existing network modules using interactive network visualisation and analysis via CytoscapeWeb. To demonstrate the utility of the database, we present examples from three fundamental biological processes (berry development, photosynthesis and flavonoid biosynthesis

Identifying key genes in rheumatoid arthritis by weighted gene co-expression network analysis.

Science.gov (United States)

Ma, Chunhui; Lv, Qi; Teng, Songsong; Yu, Yinxian; Niu, Kerun; Yi, Chengqin

2017-08-01

This study aimed to identify rheumatoid arthritis (RA) related genes based on microarray data using the WGCNA (weighted gene co-expression network analysis) method. Two gene expression profile datasets GSE55235 (10 RA samples and 10 healthy controls) and GSE77298 (16 RA samples and seven healthy controls) were downloaded from Gene Expression Omnibus database. Characteristic genes were identified using metaDE package. WGCNA was used to find disease-related networks based on gene expression correlation coefficients, and module significance was defined as the average gene significance of all genes used to assess the correlation between the module and RA status. Genes in the disease-related gene co-expression network were subject to functional annotation and pathway enrichment analysis using Database for Annotation Visualization and Integrated Discovery. Characteristic genes were also mapped to the Connectivity Map to screen small molecules. A total of 599 characteristic genes were identified. For each dataset, characteristic genes in the green, red and turquoise modules were most closely associated with RA, with gene numbers of 54, 43 and 79, respectively. These genes were enriched in totally enriched in 17 Gene Ontology terms, mainly related to immune response (CD97, FYB, CXCL1, IKBKE, CCR1, etc.), inflammatory response (CD97, CXCL1, C3AR1, CCR1, LYZ, etc.) and homeostasis (C3AR1, CCR1, PLN, CCL19, PPT1, etc.). Two small-molecule drugs sanguinarine and papaverine were predicted to have a therapeutic effect against RA. Genes related to immune response, inflammatory response and homeostasis presumably have critical roles in RA pathogenesis. Sanguinarine and papaverine have a potential therapeutic effect against RA. © 2017 Asia Pacific League of Associations for Rheumatology and John Wiley & Sons Australia, Ltd.

Co-ordinated stage-dependent enhancement of Plasmodium falciparum antioxidant enzymes and heat shock protein expression in parasites growing in oxidatively stressed or G6PD-deficient red blood cells

Directory of Open Access Journals (Sweden)

Müller Sylke

2009-05-01

Full Text Available Abstract Background Plasmodium falciparum-parasitized red blood cells (RBCs are equipped with protective antioxidant enzymes and heat shock proteins (HSPs. The latter are only considered to protect against thermal stress. Important issues are poorly explored: first, it is insufficiently known how both systems are expressed in relation to the parasite developmental stage; secondly, it is unknown whether P. falciparum HSPs are redox-responsive, in view of redox sensitivity of HSP in eukaryotic cells; thirdly, it is poorly known how the antioxidant defense machinery would respond to increased oxidative stress or inhibited antioxidant defense. Those issues are interesting as several antimalarials increase the oxidative stress or block antioxidant defense in the parasitized RBC. In addition, numerous inhibitors of HSPs are currently developed for cancer therapy and might be tested as anti-malarials. Thus, the joint disruption of the parasite antioxidant enzymes/HSP system would interfere with parasite growth and open new perspectives for anti-malaria therapy. Methods Stage-dependent mRNA expression of ten representative P. falciparum antioxidant enzymes and hsp60/70–2/70–3/75/90 was studied by quantitative real-time RT-PCR in parasites growing in normal RBCs, in RBCs oxidatively-stressed by moderate H2O2 generation and in G6PD-deficient RBCs. Protein expression of antioxidant enzymes was assayed by Western blotting. The pentosephosphate-pathway flux was measured in isolated parasites after Sendai-virus lysis of RBC membrane. Results In parasites growing in normal RBCs, mRNA expression of antioxidant enzymes and HSPs displayed co-ordinated stage-dependent modulation, being low at ring, highest at early trophozoite and again very low at schizont stage. Additional exogenous oxidative stress or growth in antioxidant blunted G6PD-deficient RBCs indicated remarkable flexibility of both systems, manifested by enhanced, co-ordinated mRNA expression of

Co-ordinated stage-dependent enhancement of Plasmodium falciparum antioxidant enzymes and heat shock protein expression in parasites growing in oxidatively stressed or G6PD-deficient red blood cells.

Science.gov (United States)

Akide-Ndunge, Oscar Bate; Tambini, Elisa; Giribaldi, Giuliana; McMillan, Paul J; Müller, Sylke; Arese, Paolo; Turrini, Francesco

2009-05-29

Plasmodium falciparum-parasitized red blood cells (RBCs) are equipped with protective antioxidant enzymes and heat shock proteins (HSPs). The latter are only considered to protect against thermal stress. Important issues are poorly explored: first, it is insufficiently known how both systems are expressed in relation to the parasite developmental stage; secondly, it is unknown whether P. falciparum HSPs are redox-responsive, in view of redox sensitivity of HSP in eukaryotic cells; thirdly, it is poorly known how the antioxidant defense machinery would respond to increased oxidative stress or inhibited antioxidant defense. Those issues are interesting as several antimalarials increase the oxidative stress or block antioxidant defense in the parasitized RBC. In addition, numerous inhibitors of HSPs are currently developed for cancer therapy and might be tested as anti-malarials. Thus, the joint disruption of the parasite antioxidant enzymes/HSP system would interfere with parasite growth and open new perspectives for anti-malaria therapy. Stage-dependent mRNA expression of ten representative P. falciparum antioxidant enzymes and hsp60/70-2/70-3/75/90 was studied by quantitative real-time RT-PCR in parasites growing in normal RBCs, in RBCs oxidatively-stressed by moderate H2O2 generation and in G6PD-deficient RBCs. Protein expression of antioxidant enzymes was assayed by Western blotting. The pentosephosphate-pathway flux was measured in isolated parasites after Sendai-virus lysis of RBC membrane. In parasites growing in normal RBCs, mRNA expression of antioxidant enzymes and HSPs displayed co-ordinated stage-dependent modulation, being low at ring, highest at early trophozoite and again very low at schizont stage. Additional exogenous oxidative stress or growth in antioxidant blunted G6PD-deficient RBCs indicated remarkable flexibility of both systems, manifested by enhanced, co-ordinated mRNA expression of antioxidant enzymes and HSPs. Protein expression of

INFCE technical co-ordinating committee documents

Energy Technology Data Exchange (ETDEWEB)

None

1980-07-01

A collection of the documents covering the period December 1977 through February 1980 submitted to or generated by the Technical Co-ordinating Comittee is presented. The documents cover primarily the organizational aspects of INFCE, but conclusions from the various Working Groups are summarized.

INFCE technical co-ordinating committee documents

International Nuclear Information System (INIS)

A collection of the documents covering the period December 1977 through February 1980 submitted to or generated by the Technical Co-ordinating Comittee is presented. The documents cover primarily the organizational aspects of INFCE, but conclusions from the various Working Trays are summarized

UK Natural Analogue Co-Ordinating Group: first annual progress report

International Nuclear Information System (INIS)

Hooker, P.J.; Chapman, N.A.

1987-11-01

The British Geological Survey is reponsible for co-ordinating the Department of the Environment's programme of natural analogue studies of radionuclide migration, a research programme that involved both UK and overseas sites. Co-ordination is achieved through the UK Natural Analogue Co-ordinating Group (NACG) which was established in October 1986. It has met three times to date and its function is to ensure that the different research projects have an integrated purpose aimed at improving and applying our understanding of natural geochemical processes in a way that will increase our confidence in long-term modelling predictions. Improved modelling prediction of radionuclide transport in the geosphere will directly benefit the performance and safety assessments of proposed radioactive waste repositories. (author)

Dominant supply chain co-ordination strategies in the Dutch aerospace industry

NARCIS (Netherlands)

Voordijk, Johannes T.; Meijboom, Bert

2005-01-01

Purpose – Firms in the aerospace industry face considerable pressure to improve co-ordination in their supply chains. The major question of the present study is what supply chain co-ordination strategies are dominant in the Dutch aerospace industry given the market environment of this industry?

How can the co-ordinate transformation method of beam matching be extended to include separately labelled collimators?

Science.gov (United States)

Morgan-Fletcher, S; McKenzie, A L

1996-03-01

The problem of matching radiation beams was tackled by Siddon in 1980 using co-ordinate transformations. Since then, the need to distinguish between individual collimators in prescriptions of treatment set-up, brought about by the widespread use of 3-D treatment planning systems and asymmetric fields, as well as a reversal of the rotation sense in the turntable co-ordinate system proposed by the International Electrotechnical Commission, have made it necessary to revisit this particular problem. This paper builds upon Siddon's general equations for the particular case of matching beams, and derives expressions for calculating treatment-unit settings which may be used in a computer program without the need to perform matrix manipulation. The expression treat the individual collimator jaws separately.

Co-ordinate expression of the pre-T-cell receptor complex and a novel immature thymocyte-specific antigen, IMT-1, during thymocyte development.

Science.gov (United States)

Tong, J J; Kishi, H; Nagata, T; Muraguchi, A

1999-01-01

Previously we described a monoclonal antibody (mAb) that reacted with a cell-surface antigen, immature thymocyte antigen-1 (IMT-1), which is expressed on thymocytes of late CD4- CD8- (double negative) to early CD4+ CD8+ (double positive) differentiation stages. In this study, we investigated the expression of IMT-1 on various cell lineages in thymus as well as in peripheral lymphoid organs. We found that IMT-1 is expressed on T-cell receptor (TCR)-betalo and TCR-deltalo thymocytes, but not on TCR-betahi, TCR-deltahi or natural killer (NK)1.1+ thymocytes, or on peripheral alpha beta or gamma delta T cells. We also investigated the kinetics of expression of IMT-1 during fetal thymocyte development and compared it with the expression of the pre-TCR complex, comprising CD3, pre-TCR-alpha (pTalpha) and TCR-beta. We found that expression of both was similar, starting at day 14.5 of gestation, peaking on day 16.5 and gradually decreasing thereafter. Furthermore, the expression of both IMT-1 and pTalpha was drastically reduced when DN thymocytes in recombination activating gene (RAG)-2-/- mice were challenged in vivo with anti-CD3 mAb. These results indicate that IMT-1 is expressed on not only immature thymocytes of alpha beta T-cell lineage but also on those of gamma delta T-cell lineage, and that the expression of IMT-1 and the pre-TCR complex is co-ordinately regulated during the alpha beta lineage thymocyte development.

FastGCN: a GPU accelerated tool for fast gene co-expression networks.

Directory of Open Access Journals (Sweden)

Meimei Liang

Full Text Available Gene co-expression networks comprise one type of valuable biological networks. Many methods and tools have been published to construct gene co-expression networks; however, most of these tools and methods are inconvenient and time consuming for large datasets. We have developed a user-friendly, accelerated and optimized tool for constructing gene co-expression networks that can fully harness the parallel nature of GPU (Graphic Processing Unit architectures. Genetic entropies were exploited to filter out genes with no or small expression changes in the raw data preprocessing step. Pearson correlation coefficients were then calculated. After that, we normalized these coefficients and employed the False Discovery Rate to control the multiple tests. At last, modules identification was conducted to construct the co-expression networks. All of these calculations were implemented on a GPU. We also compressed the coefficient matrix to save space. We compared the performance of the GPU implementation with those of multi-core CPU implementations with 16 CPU threads, single-thread C/C++ implementation and single-thread R implementation. Our results show that GPU implementation largely outperforms single-thread C/C++ implementation and single-thread R implementation, and GPU implementation outperforms multi-core CPU implementation when the number of genes increases. With the test dataset containing 16,000 genes and 590 individuals, we can achieve greater than 63 times the speed using a GPU implementation compared with a single-thread R implementation when 50 percent of genes were filtered out and about 80 times the speed when no genes were filtered out.

Building gene co-expression networks using transcriptomics data for systems biology investigations

DEFF Research Database (Denmark)

Kadarmideen, Haja; Watson-Haigh, Nathan S.

2012-01-01

Gene co-expression networks (GCN), built using high-throughput gene expression data are fundamental aspects of systems biology. The main aims of this study were to compare two popular approaches to building and analysing GCN. We use real ovine microarray transcriptomics datasets representing four......) is connected within a network. The two GCN construction methods used were, Weighted Gene Co-expression Network Analysis (WGCNA) and Partial Correlation and Information Theory (PCIT) methods. Nodes were ranked based on their connectivity measures in each of the four different networks created by WGCNA and PCIT...... (with > 20000 genes) access to large computer clusters, particularly those with larger amounts of shared memory is recommended....

Co-ordinate regulation of lactate metabolism genes in yeast: the role of the lactate permease gene JEN1.

Science.gov (United States)

Lodi, T; Fontanesi, F; Guiard, B

2002-01-01

In the yeast Saccharomyces cerevisiae, the first step in lactate metabolism is its transport across the plasma membrane, a proton symport process mediated by the product of the gene JEN1. Under aerobic conditions, the expression of JEN1 is regulated by the carbon source: the gene is repressed by glucose and induced by non-fermentable substrates. JEN1 expression is also controlled by oxygen availability, but is unaffected by the absence of haem biosynthesis. JEN1 is negatively regulated by the repressors Mig1p and Mig2p, and requires Cat8p for full derepression. In this report we demonstrate that, in addition to these regulators, the Hap2/3/4/5 complex interacts specifically with a CAAT-box element in the JEN1 promoter, and acts to derepress JEN1 expression. We also provide evidence for transcriptional stimulation of JEN1 by the protein kinase Snf1p. Data are presented which provide a better understanding of the molecular mechanisms implicated in the co-regulation of genes involved in the metabolism of lactate.

Array2BIO: from microarray expression data to functional annotation of co-regulated genes

Directory of Open Access Journals (Sweden)

Rasley Amy

2006-06-01

Full Text Available Abstract Background There are several isolated tools for partial analysis of microarray expression data. To provide an integrative, easy-to-use and automated toolkit for the analysis of Affymetrix microarray expression data we have developed Array2BIO, an application that couples several analytical methods into a single web based utility. Results Array2BIO converts raw intensities into probe expression values, automatically maps those to genes, and subsequently identifies groups of co-expressed genes using two complementary approaches: (1 comparative analysis of signal versus control and (2 clustering analysis of gene expression across different conditions. The identified genes are assigned to functional categories based on Gene Ontology classification and KEGG protein interaction pathways. Array2BIO reliably handles low-expressor genes and provides a set of statistical methods for quantifying expression levels, including Benjamini-Hochberg and Bonferroni multiple testing corrections. An automated interface with the ECR Browser provides evolutionary conservation analysis for the identified gene loci while the interconnection with Crème allows prediction of gene regulatory elements that underlie observed expression patterns. Conclusion We have developed Array2BIO – a web based tool for rapid comprehensive analysis of Affymetrix microarray expression data, which also allows users to link expression data to Dcode.org comparative genomics tools and integrates a system for translating co-expression data into mechanisms of gene co-regulation. Array2BIO is publicly available at http://array2bio.dcode.org.

In-silico gene co-expression network analysis in Paracoccidioides brasiliensis with reference to haloacid dehalogenase superfamily hydrolase gene

Directory of Open Access Journals (Sweden)

Raghunath Satpathy

2015-01-01

Full Text Available Context: Paracoccidioides brasiliensis, a dimorphic fungus is the causative agent of paracoccidioidomycosis, a disease globally affecting millions of people. The haloacid dehalogenase (HAD superfamily hydrolases enzyme in the fungi, in particular, is known to be responsible in the pathogenesis by adhering to the tissue. Hence, identification of novel drug targets is essential. Aims: In-silico based identification of co-expressed genes along with HAD superfamily hydrolase in P. brasiliensis during the morphogenesis from mycelium to yeast to identify possible genes as drug targets. Materials and Methods: In total, four datasets were retrieved from the NCBI-gene expression omnibus (GEO database, each containing 4340 genes, followed by gene filtration expression of the data set. Further co-expression (CE study was performed individually and then a combination these genes were visualized in the Cytoscape 2. 8.3. Statistical Analysis Used: Mean and standard deviation value of the HAD superfamily hydrolase gene was obtained from the expression data and this value was subsequently used for the CE calculation purpose by selecting specific correlation power and filtering threshold. Results: The 23 genes that were thus obtained are common with respect to the HAD superfamily hydrolase gene. A significant network was selected from the Cytoscape network visualization that contains total 7 genes out of which 5 genes, which do not have significant protein hits, obtained from gene annotation of the expressed sequence tags by BLAST X. For all the protein PSI-BLAST was performed against human genome to find the homology. Conclusions: The gene co-expression network was obtained with respect to HAD superfamily dehalogenase gene in P. Brasiliensis.

Using gene co-expression network analysis to predict biomarkers for chronic lymphocytic leukemia

Directory of Open Access Journals (Sweden)

Borlawsky Tara B

2010-10-01

Full Text Available Abstract Background Chronic lymphocytic leukemia (CLL is the most common adult leukemia. It is a highly heterogeneous disease, and can be divided roughly into indolent and progressive stages based on classic clinical markers. Immunoglobin heavy chain variable region (IgVH mutational status was found to be associated with patient survival outcome, and biomarkers linked to the IgVH status has been a focus in the CLL prognosis research field. However, biomarkers highly correlated with IgVH mutational status which can accurately predict the survival outcome are yet to be discovered. Results In this paper, we investigate the use of gene co-expression network analysis to identify potential biomarkers for CLL. Specifically we focused on the co-expression network involving ZAP70, a well characterized biomarker for CLL. We selected 23 microarray datasets corresponding to multiple types of cancer from the Gene Expression Omnibus (GEO and used the frequent network mining algorithm CODENSE to identify highly connected gene co-expression networks spanning the entire genome, then evaluated the genes in the co-expression network in which ZAP70 is involved. We then applied a set of feature selection methods to further select genes which are capable of predicting IgVH mutation status from the ZAP70 co-expression network. Conclusions We have identified a set of genes that are potential CLL prognostic biomarkers IL2RB, CD8A, CD247, LAG3 and KLRK1, which can predict CLL patient IgVH mutational status with high accuracies. Their prognostic capabilities were cross-validated by applying these biomarker candidates to classify patients into different outcome groups using a CLL microarray datasets with clinical information.

IAEA co-ordinated technical support programme to the NIS

International Nuclear Information System (INIS)

Olsen, R.; Murakami, K.; Blacker, C.; Sharma, S.K.

1999-01-01

With most Newly Independent States (NIS) of the former Soviet Union becoming parties to the Non-Proliferation Treaty as Non-Nuclear Weapon States, there has been an acute need in these states for considerable assistance for the establishment of the necessary structure and resources to ensure that their commitments to non-proliferation are fully implemented in a timely manner. A number of IAEA Member States have offered and are now providing assistance to the NIS on a bilateral level to set up an appropriate State System of Accounting and Control (SSAC) which includes Import/Export Control and Physical Protection of Nuclear Material in each state. The IAEA and these Member States established the Co-ordinated Technical Support Programme (CTSP) to ensure that the support given to the NIS was done in a co-ordinated and transparent manner and to avoid duplication of effort. The IAEA has played a coordinating role for the past 5 years by helping to identify detailed needs in individual States, by providing a platform for Member States to identify areas where they could provide the optimum support, and in developing and preparing the Co-ordinated Technical Support Plans. The IAEA organises annual meetings in Vienna attended by all donor and recipient countries to review the focus and implementation status of the co-ordinated technical support activities. A position statement is made by each donor and recipient country, and views and experiences are exchanged. The contents of the CTSPs and the role of the Agency in monitoring the progress of the individual tasks are reviewed in this paper. A summary comparing the implementation status of the Programme by each country is presented. (author)

Gene Co-expression Analysis to Characterize Genes Related to Marbling Trait in Hanwoo (Korean) Cattle.

Science.gov (United States)

Lim, Dajeong; Lee, Seung-Hwan; Kim, Nam-Kuk; Cho, Yong-Min; Chai, Han-Ha; Seong, Hwan-Hoo; Kim, Heebal

2013-01-01

Marbling (intramuscular fat) is an important trait that affects meat quality and is a casual factor determining the price of beef in the Korean beef market. It is a complex trait and has many biological pathways related to muscle and fat. There is a need to identify functional modules or genes related to marbling traits and investigate their relationships through a weighted gene co-expression network analysis based on the system level. Therefore, we investigated the co-expression relationships of genes related to the 'marbling score' trait and systemically analyzed the network topology in Hanwoo (Korean cattle). As a result, we determined 3 modules (gene groups) that showed statistically significant results for marbling score. In particular, one module (denoted as red) has a statistically significant result for marbling score (p = 0.008) and intramuscular fat (p = 0.02) and water capacity (p = 0.006). From functional enrichment and relationship analysis of the red module, the pathway hub genes (IL6, CHRNE, RB1, INHBA and NPPA) have a direct interaction relationship and share the biological functions related to fat or muscle, such as adipogenesis or muscle growth. This is the first gene network study with m.logissimus in Hanwoo to observe co-expression patterns in divergent marbling phenotypes. It may provide insights into the functional mechanisms of the marbling trait.

Gene Co-expression Analysis to Characterize Genes Related to Marbling Trait in Hanwoo (Korean Cattle

Directory of Open Access Journals (Sweden)

Dajeong Lim

2013-01-01

Full Text Available Marbling (intramuscular fat is an important trait that affects meat quality and is a casual factor determining the price of beef in the Korean beef market. It is a complex trait and has many biological pathways related to muscle and fat. There is a need to identify functional modules or genes related to marbling traits and investigate their relationships through a weighted gene co-expression network analysis based on the system level. Therefore, we investigated the co-expression relationships of genes related to the ‘marbling score’ trait and systemically analyzed the network topology in Hanwoo (Korean cattle. As a result, we determined 3 modules (gene groups that showed statistically significant results for marbling score. In particular, one module (denoted as red has a statistically significant result for marbling score (p = 0.008 and intramuscular fat (p = 0.02 and water capacity (p = 0.006. From functional enrichment and relationship analysis of the red module, the pathway hub genes (IL6, CHRNE, RB1, INHBA and NPPA have a direct interaction relationship and share the biological functions related to fat or muscle, such as adipogenesis or muscle growth. This is the first gene network study with m.logissimus in Hanwoo to observe co-expression patterns in divergent marbling phenotypes. It may provide insights into the functional mechanisms of the marbling trait.

Disease gene characterization through large-scale co-expression analysis.

Directory of Open Access Journals (Sweden)

Allen Day

2009-12-01

Full Text Available In the post genome era, a major goal of biology is the identification of specific roles for individual genes. We report a new genomic tool for gene characterization, the UCLA Gene Expression Tool (UGET.Celsius, the largest co-normalized microarray dataset of Affymetrix based gene expression, was used to calculate the correlation between all possible gene pairs on all platforms, and generate stored indexes in a web searchable format. The size of Celsius makes UGET a powerful gene characterization tool. Using a small seed list of known cartilage-selective genes, UGET extended the list of known genes by identifying 32 new highly cartilage-selective genes. Of these, 7 of 10 tested were validated by qPCR including the novel cartilage-specific genes SDK2 and FLJ41170. In addition, we retrospectively tested UGET and other gene expression based prioritization tools to identify disease-causing genes within known linkage intervals. We first demonstrated this utility with UGET using genetically heterogeneous disorders such as Joubert syndrome, microcephaly, neuropsychiatric disorders and type 2 limb girdle muscular dystrophy (LGMD2 and then compared UGET to other gene expression based prioritization programs which use small but discrete and well annotated datasets. Finally, we observed a significantly higher gene correlation shared between genes in disease networks associated with similar complex or Mendelian disorders.UGET is an invaluable resource for a geneticist that permits the rapid inclusion of expression criteria from one to hundreds of genes in genomic intervals linked to disease. By using thousands of arrays UGET annotates and prioritizes genes better than other tools especially with rare tissue disorders or complex multi-tissue biological processes. This information can be critical in prioritization of candidate genes for sequence analysis.

Co-ordinated research programme on applications of stable isotope tracers in human nutrition research

International Nuclear Information System (INIS)

1992-01-01

This document provides a very brief report on the final Research Co-ordination Meeting of this Co-ordinated Research Project (CRP): the final report on the CRP will be published by the IAEA in the IAEA-TECDOC series. The present document contains a detailed proposal for a new Co-ordinated Research Programme on ''Stable Isotope Tracer Techniques for Studies on Protein-Energy Interactions'', and a brief series of notes on stable isotopic methods for investigating protein and amino-acid metabolism in man. Refs

Network statistics of genetically-driven gene co-expression modules in mouse crosses

Directory of Open Access Journals (Sweden)

Marie-Pier eScott-Boyer

2013-12-01

Full Text Available In biology, networks are used in different contexts as ways to represent relationships between entities, such as for instance interactions between genes, proteins or metabolites. Despite progress in the analysis of such networks and their potential to better understand the collective impact of genes on complex traits, one remaining challenge is to establish the biologic validity of gene co-expression networks and to determine what governs their organization. We used WGCNA to construct and analyze seven gene expression datasets from several tissues of mouse recombinant inbred strains (RIS. For six out of the 7 networks, we found that linkage to module QTLs (mQTLs could be established for 29.3% of gene co-expression modules detected in the several mouse RIS. For about 74.6% of such genetically-linked modules, the mQTL was on the same chromosome as the one contributing most genes to the module, with genes originating from that chromosome showing higher connectivity than other genes in the modules. Such modules (that we considered as genetically-driven had network statistic properties (density, centralization and heterogeneity that set them apart from other modules in the network. Altogether, a sizeable portion of gene co-expression modules detected in mouse RIS panels had genetic determinants as their main organizing principle. In addition to providing a biologic interpretation validation for these modules, these genetic determinants imparted on them particular properties that set them apart from other modules in the network, to the point that they can be predicted to a large extent on the basis of their network statistics.

Co-ordinate activation of lipogenic enzymes in hepatocellular carcinoma.

Science.gov (United States)

Yahagi, Naoya; Shimano, Hitoshi; Hasegawa, Kiyoshi; Ohashi, Kenichi; Matsuzaka, Takashi; Najima, Yuho; Sekiya, Motohiro; Tomita, Sachiko; Okazaki, Hiroaki; Tamura, Yoshiaki; Iizuka, Yoko; Ohashi, Ken; Nagai, Ryozo; Ishibashi, Shun; Kadowaki, Takashi; Makuuchi, Masatoshi; Ohnishi, Shin; Osuga, Jun-ichi; Yamada, Nobuhiro

2005-06-01

Hepatocellular carcinoma is a very common neoplastic disease in countries where hepatitis viruses B and/or C are prevalent. Small hepatocellular carcinoma lesions detected by ultrasonography at an early stage are often hyperechoic because they are composed of well-differentiated cancer cells that are rich in triglyceride droplets. The triglyceride content of hepatocytes depends in part on the rate of lipogenesis. Key lipogenic enzymes, such as fatty acid synthase, are co-ordinately regulated at the transcriptional level. We therefore examined the mRNA expression of lipogenic enzymes in human hepatocellular carcinoma samples from 10 patients who had undergone surgical resection. All of the samples exhibited marked elevation of expression of mRNA for lipogenic enzymes, such as fatty acid synthase, acetyl-CoA carboxylase and ATP citrate lyase, compared with surrounding non-cancerous liver tissue. In contrast, the changes in mRNA expression of SREBP-1, a transcription factor that regulates a battery of lipogenic enzymes, did not show a consistent trend. In some cases where SREBP-1 was elevated, the main contributing isoform was SREBP-1c rather than SREBP-1a. Thus, lipogenic enzymes are markedly induced in hepatocellular carcinomas, and in some cases SREBP-1c is involved in this activation.

About local fractional three-dimensional compressible Navier-Stokes equations in Cantor-type cylindrical co-ordinate system

Directory of Open Access Journals (Sweden)

Gao Guo-Ping

2016-01-01

Full Text Available In this article, we investigate the local fractional 3-D compressible Navier-Stokes equation via local fractional derivative. We use the Cantor-type cylindrical co-ordinate method to transfer 3-D compressible Navier-Stokes equation from the Cantorian co-ordinate system to the Cantor-type cylindrical co-ordinate system.

Care co-ordination for older people in the third sector: scoping the evidence.

Science.gov (United States)

Abendstern, Michele; Hughes, Jane; Jasper, Rowan; Sutcliffe, Caroline; Challis, David

2018-05-01

The third sector has played a significant role internationally in the delivery of adult social care services for many years. Its contribution to care co-ordination activities for older people, however, in England and elsewhere, is relatively unknown. A scoping review was therefore conducted to ascertain the character of the literature, the nature and extent of third sector care co-ordination activity, and to identify evidence gaps. It was undertaken between autumn 2013 and summer 2014 and updated with additional searches in 2016. Electronic and manual searches of international literature using distinct terms for different approaches to care co-ordination were undertaken. From a total of 835 papers, 26 met inclusion criteria. Data were organised in relation to care co-ordination approaches, types of third sector organisation and care recipients. Papers were predominantly from the UK and published this century. Key findings included that: a minority of literature focused specifically on older people and that those doing so described only one care co-ordination approach; third sector services tended to be associated with independence and person-centred practice; and working with the statutory sector, a prerequisite of care co-ordination, was challenging and required a range of features to be in place to support effective partnerships. Strengths and weaknesses of care co-ordination practice in the third sector according to key stakeholder groups were also highlighted. Areas for future research included the need for: a specific focus on older people's experiences; an investigation of workforce issues; detailed examination of third sector practices, outcomes and costs; interactions with the statutory sector; and an examination of quality assurance systems and their appropriateness to third sector practice. The main implication of the findings is a need to nurture variety within the third sector in order to provide older people and other adults with the range of service

Case management for high-intensity service users: towards a relational approach to care co-ordination.

Science.gov (United States)

McEvoy, Phil; Escott, Diane; Bee, Penny

2011-01-01

This study is based on a formative evaluation of a case management service for high-intensity service users in Northern England. The evaluation had three main purposes: (i) to assess the quality of the organisational infrastructure; (ii) to obtain a better understanding of the key influences that played a role in shaping the development of the service; and (iii) to identify potential changes in practice that may help to improve the quality of service provision. The evaluation was informed by Gittell's relational co-ordination theory, which focuses upon cross-boundary working practices that facilitate task integration. The Assessment of Chronic Illness Care Survey was used to assess the organisational infrastructure and qualitative interviews with front line staff were conducted to explore the key influences that shaped the development of the service. A high level of strategic commitment and political support for integrated working was identified. However, the quality of care co-ordination was variable. The most prominent operational factor that appeared to influence the scope and quality of care co-ordination was the pattern of interaction between the case managers and their co-workers. The co-ordination of patient care was much more effective in integrated co-ordination networks. Key features included clearly defined, task focussed, relational workspaces with interactive forums where case managers could engage with co-workers in discussions about the management of interdependent care activities. In dispersed co-ordination networks with fewer relational workspaces, the case managers struggled to work as effectively. The evaluation concluded that the creation of flexible and efficient task focused relational workspaces that are systemically managed and adequately resourced could help to improve the quality of care co-ordination, particularly in dispersed networks. © 2010 Blackwell Publishing Ltd.

ITER co-ordinated technical activities

International Nuclear Information System (INIS)

2001-01-01

As agreed upon between the ITER Engineering Design Activities (EDA) Parties 'Co-ordinated Technical Activities' (CTA) means technical activities which are deemed necessary to maintain the integrity of the international project, so as to prepare for the ITER joint implementation. The scope of these activities includes design adaptation to the specific site conditions, safety analysis and licensing preparation that are based on specific site offers, evaluation of cost and construction schedule, preparation of procurement documents and other issues raised by the Parties collectively, whilst assuring the coherence of the ITER project including design control

Co-ordinated research programme applications of stable isotope tracers in human nutrition research

International Nuclear Information System (INIS)

1992-01-01

The objective of this Co-ordinated Research Programme is to help establish competence in the use of stable isotope techniques, particularly in developing countries. This report summarizes the discussions that took, place during the Second Research Co-ordination Meeting, held in Bangalore in November 1990. Working papers presented by the participants are included as annexes. Refs, figs and tabs

Information Design for Synchronization and Co-ordination of Modern, Complex, Multi-National Operations

Science.gov (United States)

2011-06-01

1 16th ICCRTS Information design for synchronization and co-ordination of modern, complex, multi- national operations “Collective C2 in...REPORT DATE JUN 2011 2. REPORT TYPE 3. DATES COVERED 00-00-2011 to 00-00-2011 4. TITLE AND SUBTITLE Information design for synchronization and co...at 11th ICCRTS) who emphasise that information needs to be designed, not merely found or catalogued, to achieve synchronizations and co-ordinations

Lipid binding to cytoglobin leads to a change in haem co-ordination: a role for cytoglobin in lipid signalling of oxidative stress.

Science.gov (United States)

Reeder, Brandon J; Svistunenko, Dimitri A; Wilson, Michael T

2011-03-15

Cytoglobin is a recently discovered hexa-co-ordinate haemoglobin that does not appear to function as a classical oxygen-binding protein. Its function is unknown and studies on the effects of changes in its expression have not decisively determined its role within the cell. In the present paper, we report that the protein is transformed from hexa-co-ordinate to penta-co-ordinate on binding a lipid molecule. This transformation occurs with the ferric oxidation state of the protein, but not the ferrous state, indicating that this process only occurs under an oxidative environment and may thus be related to redox-linked cell signalling mechanisms. Oleate binds to the protein in a 1:1 stoichiometry and with high affinity (K(d)=0.7 μM); however, stopped-flow kinetic measurements yield a K(d) value of 110 μM. The discrepancy between these K(d) values may be rationalized by recognizing that cytoglobin is a disulfide-linked dimer and invoking co-operativity in oleate binding. The lipid-induced transformation of cytoglobin from hexa-co-ordinate to penta-co-ordinate does not occur with similar hexa-co-ordinate haemoglobins such as neuroglobin, and therefore appears to be a unique property of cytoglobin among the haemoglobin superfamily. The lipid-derived transformation may explain why cytoglobin has enhanced peroxidatic activity, converting lipids into various oxidized products, a property virtually absent from neuroglobin and much decreased in myoglobin. We propose that the binding of ferric cytoglobin to lipids and their subsequent transformation may be integral to the physiological function of cytoglobin, generating cell signalling lipid molecules under an oxidative environment.

Evaluation of endogenous control gene(s) for gene expression studies in human blood exposed to 60Co γ-rays ex vivo

International Nuclear Information System (INIS)

Vaiphei, S. Thangminlal; Keppen, Joshua; Nongrum, Saibadaiahun; Sharan, R.N.; Chaubey, R.C.; Kma, L.

2015-01-01

In gene expression studies, it is critical to normalize data using a stably expressed endogenous control gene in order to obtain accurate and reliable results. However, we currently do not have a universally applied endogenous control gene for normalization of data for gene expression studies, particularly those involving 60 Co γ-ray-exposed human blood samples. In this study, a comparative assessment of the gene expression of six widely used housekeeping endogenous control genes, namely 18S, ACTB, B2M, GAPDH, MT-ATP6 and CDKN1A, was undertaken for a range of 60 Co γ-ray doses (0.5, 1.0, 2.0 and 4.0 Gy) at 8.4 Gy min -1 at 0 and 24 h post-irradiation time intervals. Using the NormFinder algorithm, real-time PCR data obtained from six individuals (three males and three females) were analyzed with respect to the threshold cycle (Ct) value and abundance, ΔCt pair-wise comparison, intra- and inter-group variability assessments, etc. GAPDH, either alone or in combination with 18S, was found to be the most suitable endogenous control gene and should be used in gene expression studies, especially those involving qPCR of γ-ray-exposed human blood samples. (author)

A gene co-expression network in whole blood of schizophrenia patients is independent of antipsychotic-use and enriched for brain-expressed genes

DEFF Research Database (Denmark)

de Jong, Simone; Boks, Marco P M; Fuller, Tova F

2012-01-01

Despite large-scale genome-wide association studies (GWAS), the underlying genes for schizophrenia are largely unknown. Additional approaches are therefore required to identify the genetic background of this disorder. Here we report findings from a large gene expression study in peripheral blood...... of schizophrenia patients and controls. We applied a systems biology approach to genome-wide expression data from whole blood of 92 medicated and 29 antipsychotic-free schizophrenia patients and 118 healthy controls. We show that gene expression profiling in whole blood can identify twelve large gene co......, and regulated by the major histocompatibility (MHC) complex, which is intriguing in light of the fact that common allelic variants from the MHC region have been implicated in schizophrenia. This suggests that the MHC increases schizophrenia susceptibility via altered gene expression of regulatory genes...

A powerful nonparametric method for detecting differentially co-expressed genes: distance correlation screening and edge-count test.

Science.gov (United States)

Zhang, Qingyang

2018-05-16

Differential co-expression analysis, as a complement of differential expression analysis, offers significant insights into the changes in molecular mechanism of different phenotypes. A prevailing approach to detecting differentially co-expressed genes is to compare Pearson's correlation coefficients in two phenotypes. However, due to the limitations of Pearson's correlation measure, this approach lacks the power to detect nonlinear changes in gene co-expression which is common in gene regulatory networks. In this work, a new nonparametric procedure is proposed to search differentially co-expressed gene pairs in different phenotypes from large-scale data. Our computational pipeline consisted of two main steps, a screening step and a testing step. The screening step is to reduce the search space by filtering out all the independent gene pairs using distance correlation measure. In the testing step, we compare the gene co-expression patterns in different phenotypes by a recently developed edge-count test. Both steps are distribution-free and targeting nonlinear relations. We illustrate the promise of the new approach by analyzing the Cancer Genome Atlas data and the METABRIC data for breast cancer subtypes. Compared with some existing methods, the new method is more powerful in detecting nonlinear type of differential co-expressions. The distance correlation screening can greatly improve computational efficiency, facilitating its application to large data sets.

Information on Nea programmes on nuclear energy and civil society and their co-ordination

International Nuclear Information System (INIS)

Mays, C.; Riotte, H.

2004-01-01

At its session in May 2002, the Steering Committee for Nuclear Energy welcomed the activities that the NEA standing technical committees were carrying out in the field of nuclear energy and civil society, and agreed on the value of existing co-ordination among them. Tile Committee asked the Secretariat to prepare an information document on such co-ordination activities. With this in mind, the present room document offers an up-to-date account of relevant NEA activities and their co-ordination, pending a broader review of NEA's involvement in the area of nuclear energy and civil society, in the context of the NEA Strategic Plan at an appropriate time. (author)

On three-dimensional incompressible Navier-Stokes fluid on cantor sets in spherical Cantor type co-ordinate system

Directory of Open Access Journals (Sweden)

Meng Zhi-Jun

2016-01-01

Full Text Available This paper addresses the systems of the incompressible Navier-Stokes equations on Cantor sets without the external force involving the fractal heat-conduction problem vial local fractional derivative. The spherical Cantor type co-ordinate method is used to transfer the incompressible Navier-Stokes equation from the Cantorian co-ordinate system into the spherical Cantor type co-ordinate system.

Weighted gene co-expression network analysis of expression data of monozygotic twins identifies specific modules and hub genes related to BMI.

Science.gov (United States)

Wang, Weijing; Jiang, Wenjie; Hou, Lin; Duan, Haiping; Wu, Yili; Xu, Chunsheng; Tan, Qihua; Li, Shuxia; Zhang, Dongfeng

2017-11-13

The therapeutic management of obesity is challenging, hence further elucidating the underlying mechanisms of obesity development and identifying new diagnostic biomarkers and therapeutic targets are urgent and necessary. Here, we performed differential gene expression analysis and weighted gene co-expression network analysis (WGCNA) to identify significant genes and specific modules related to BMI based on gene expression profile data of 7 discordant monozygotic twins. In the differential gene expression analysis, it appeared that 32 differentially expressed genes (DEGs) were with a trend of up-regulation in twins with higher BMI when compared to their siblings. Categories of positive regulation of nitric-oxide synthase biosynthetic process, positive regulation of NF-kappa B import into nucleus, and peroxidase activity were significantly enriched within GO database and NF-kappa B signaling pathway within KEGG database. DEGs of NAMPT, TLR9, PTGS2, HBD, and PCSK1N might be associated with obesity. In the WGCNA, among the total 20 distinct co-expression modules identified, coral1 module (68 genes) had the strongest positive correlation with BMI (r = 0.56, P = 0.04) and disease status (r = 0.56, P = 0.04). Categories of positive regulation of phospholipase activity, high-density lipoprotein particle clearance, chylomicron remnant clearance, reverse cholesterol transport, intermediate-density lipoprotein particle, chylomicron, low-density lipoprotein particle, very-low-density lipoprotein particle, voltage-gated potassium channel complex, cholesterol transporter activity, and neuropeptide hormone activity were significantly enriched within GO database for this module. And alcoholism and cell adhesion molecules pathways were significantly enriched within KEGG database. Several hub genes, such as GAL, ASB9, NPPB, TBX2, IL17C, APOE, ABCG4, and APOC2 were also identified. The module eigengene of saddlebrown module (212 genes) was also significantly

Evaluation of endogenous control gene(s) for gene expression studies in human blood exposed to 60Co γ-rays ex vivo.

Science.gov (United States)

Vaiphei, S Thangminlal; Keppen, Joshua; Nongrum, Saibadaiahun; Chaubey, R C; Kma, L; Sharan, R N

2015-01-01

In gene expression studies, it is critical to normalize data using a stably expressed endogenous control gene in order to obtain accurate and reliable results. However, we currently do not have a universally applied endogenous control gene for normalization of data for gene expression studies, particularly those involving (60)Co γ-ray-exposed human blood samples. In this study, a comparative assessment of the gene expression of six widely used housekeeping endogenous control genes, namely 18S, ACTB, B2M, GAPDH, MT-ATP6 and CDKN1A, was undertaken for a range of (60)Co γ-ray doses (0.5, 1.0, 2.0 and 4.0 Gy) at 8.4 Gy min(-1) at 0 and 24 h post-irradiation time intervals. Using the NormFinder algorithm, real-time PCR data obtained from six individuals (three males and three females) were analyzed with respect to the threshold cycle (Ct) value and abundance, ΔCt pair-wise comparison, intra- and inter-group variability assessments, etc. GAPDH, either alone or in combination with 18S, was found to be the most suitable endogenous control gene and should be used in gene expression studies, especially those involving qPCR of γ-ray-exposed human blood samples. © The Author 2014. Published by Oxford University Press on behalf of The Japan Radiation Research Society and Japanese Society for Radiation Oncology.

An Integrated Model of Co-ordinated Community-Based Care.

Science.gov (United States)

Scharlach, Andrew E; Graham, Carrie L; Berridge, Clara

2015-08-01

Co-ordinated approaches to community-based care are a central component of current and proposed efforts to help vulnerable older adults obtain needed services and supports and reduce unnecessary use of health care resources. This study examines ElderHelp Concierge Club, an integrated community-based care model that includes comprehensive personal and environmental assessment, multilevel care co-ordination, a mix of professional and volunteer service providers, and a capitated, income-adjusted fee model. Evaluation includes a retrospective study (n = 96) of service use and perceived program impact, and a prospective study (n = 21) of changes in participant physical and social well-being and health services utilization. Over the period of this study, participants showed greater mobility, greater ability to meet household needs, greater access to health care, reduced social isolation, reduced home hazards, fewer falls, and greater perceived ability to obtain assistance needed to age in place. This study provides preliminary evidence that an integrated multilevel care co-ordination approach may be an effective and efficient model for serving vulnerable community-based elders, especially low and moderate-income elders who otherwise could not afford the cost of care. The findings suggest the need for multisite controlled studies to more rigorously evaluate program impacts and the optimal mix of various program components. © The Author 2014. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Co-ordinate control of synthesis of mitochondrial and non-mitochondrial hemoproteins: a binding site for the HAP1 (CYP1) protein in the UAS region of the yeast catalase T gene (CTT1).

Science.gov (United States)

Winkler, H; Adam, G; Mattes, E; Schanz, M; Hartig, A; Ruis, H

1988-01-01

Control of expression of the Saccharomyces cerevisiae CTT1 (catalase T) gene by the HAP1 (CYP1) gene, a mediator of heme control of mitochondrial cytochromes, was studied. Expression of a CTT1-lacZ fusion in a hap1 mutant showed that the CTT1 promoter is under HAP1 control. As demonstrated by a gel retardation assay, the HAP1 protein binds to a heme control region of the CTT1 gene. This binding in vitro is stimulated by hemin. The HAP1-binding sequence was localized by using DNA fragments spanning different regions, by DNase I footprinting and by methylation interference of DNA-protein binding. The binding site was compared to the HAP1-binding sequences previously characterized in detail (UAS1CYC1, UASCYC7). There is strikingly little similarity between the three sequences, which have only four of those 23 bp in common which are protected from DNase I digestion. However, the pattern of major and minor groove contacts in the complex is quite similar in all three cases. The results obtained show that there is true co-ordinate control of expression of mitochondrial cytochromes and at least some extra-mitochondrial hemoproteins. Heme acts as a metabolic signal in this coordination, which is mediated by the HAP1 protein. Images PMID:2844525

Co-ordinated research activities: Annual report and statistics for 2003

International Nuclear Information System (INIS)

2004-07-01

Article III of the IAEA Statute authorises the Agency to encourage and assist research on, and development and practical application of, atomic energy for peaceful purposes throughout the world and to foster the exchange of scientific and technical information, as well as the exchange of scientists in the field of peaceful uses of atomic energy. The research supported by the Agency is within the framework of the Agency's programmes, sub-programmes and projects that are listed in the approved Programme and Budget of the Agency. These co-ordinated research activities are normally implemented through Co-ordinated Research Projects (CRPs) that bring together research institutes in both developing and developed Member States to collaborate on the research topic of interest. The Agency may also respond to proposals from institutes for participation in the research activities by awarding individual contracts not related to a CRP. A small portion of available funds is used to finance individual projects, which deal with topics covered by the Agency's scientific programme. The Agency also supports several Doctoral CRPs. This new, optional type of CRP has been designed to strengthen promotion of research on nuclear technologies in developing Member States through pair building between agreement holders and contract holders. These CRPs include a PhD training programme at the contract holders' institutions. Three doctoral CRPs are currently being carried out by the Human Health programme. Further information on the Agency's co-ordinated research activities, including current information on CRPs and programme areas supported, information on policies and procedures and the administration of the activities is contained in the Agency's website at http://www-crp.iaea.org. The co-ordinated research activities reported in this document are conducted in support of the following Agency programmes: Nuclear Power; Nuclear Fuel Cycle and Material Technologies; Analysis for Sustainable

Co-ordinated research activities: Annual report and statistics for 2003

Energy Technology Data Exchange (ETDEWEB)

NONE

2004-07-15

Article III of the IAEA Statute authorises the Agency to encourage and assist research on, and development and practical application of, atomic energy for peaceful purposes throughout the world and to foster the exchange of scientific and technical information, as well as the exchange of scientists in the field of peaceful uses of atomic energy. The research supported by the Agency is within the framework of the Agency's programmes, sub-programmes and projects that are listed in the approved Programme and Budget of the Agency. These co-ordinated research activities are normally implemented through Co-ordinated Research Projects (CRPs) that bring together research institutes in both developing and developed Member States to collaborate on the research topic of interest. The Agency may also respond to proposals from institutes for participation in the research activities by awarding individual contracts not related to a CRP. A small portion of available funds is used to finance individual projects, which deal with topics covered by the Agency's scientific programme. The Agency also supports several Doctoral CRPs. This new, optional type of CRP has been designed to strengthen promotion of research on nuclear technologies in developing Member States through pair building between agreement holders and contract holders. These CRPs include a PhD training programme at the contract holders' institutions. Three doctoral CRPs are currently being carried out by the Human Health programme. Further information on the Agency's co-ordinated research activities, including current information on CRPs and programme areas supported, information on policies and procedures and the administration of the activities is contained in the Agency's website at http://www-crp.iaea.org. The co-ordinated research activities reported in this document are conducted in support of the following Agency programmes: Nuclear Power; Nuclear Fuel Cycle and Material Technologies; Analysis for Sustainable

Uncovering co-expression gene network modules regulating fruit acidity in diverse apples.

Science.gov (United States)

Bai, Yang; Dougherty, Laura; Cheng, Lailiang; Zhong, Gan-Yuan; Xu, Kenong

2015-08-16

Acidity is a major contributor to fruit quality. Several organic acids are present in apple fruit, but malic acid is predominant and determines fruit acidity. The trait is largely controlled by the Malic acid (Ma) locus, underpinning which Ma1 that putatively encodes a vacuolar aluminum-activated malate transporter1 (ALMT1)-like protein is a strong candidate gene. We hypothesize that fruit acidity is governed by a gene network in which Ma1 is key member. The goal of this study is to identify the gene network and the potential mechanisms through which the network operates. Guided by Ma1, we analyzed the transcriptomes of mature fruit of contrasting acidity from six apple accessions of genotype Ma_ (MaMa or Mama) and four of mama using RNA-seq and identified 1301 fruit acidity associated genes, among which 18 were most significant acidity genes (MSAGs). Network inferring using weighted gene co-expression network analysis (WGCNA) revealed five co-expression gene network modules of significant (P acidity. Overall, this study provides important insight into the Ma1-mediated gene network controlling acidity in mature apple fruit of diverse genetic background.

First IAEA research co-ordination meeting on 'Tritium inventory in fusion reactors'. Summary report

International Nuclear Information System (INIS)

Clark, R.E.H.

2003-02-01

The proceedings and conclusions of the first Research Co-ordination Meeting on 'Tritium Inventory in Fusion Reactors', held on November 4-6, 2002 at the IAEA Headquarters in Vienna are briefly described. This report includes a summary of the presentations made by the meeting participants and the specific goals set by the participants of the Co-ordinated Research Project (CRP). (author)

A stochastic model for identifying differential gene pair co-expression patterns in prostate cancer progression

Directory of Open Access Journals (Sweden)

Mao Yu

2009-07-01

Full Text Available Abstract Background The identification of gene differential co-expression patterns between cancer stages is a newly developing method to reveal the underlying molecular mechanisms of carcinogenesis. Most researches of this subject lack an algorithm useful for performing a statistical significance assessment involving cancer progression. Lacking this specific algorithm is apparently absent in identifying precise gene pairs correlating to cancer progression. Results In this investigation we studied gene pair co-expression change by using a stochastic process model for approximating the underlying dynamic procedure of the co-expression change during cancer progression. Also, we presented a novel analytical method named 'Stochastic process model for Identifying differentially co-expressed Gene pair' (SIG method. This method has been applied to two well known prostate cancer data sets: hormone sensitive versus hormone resistant, and healthy versus cancerous. From these data sets, 428,582 gene pairs and 303,992 gene pairs were identified respectively. Afterwards, we used two different current statistical methods to the same data sets, which were developed to identify gene pair differential co-expression and did not consider cancer progression in algorithm. We then compared these results from three different perspectives: progression analysis, gene pair identification effectiveness analysis, and pathway enrichment analysis. Statistical methods were used to quantify the quality and performance of these different perspectives. They included: Re-identification Scale (RS and Progression Score (PS in progression analysis, True Positive Rate (TPR in gene pair analysis, and Pathway Enrichment Score (PES in pathway analysis. Our results show small values of RS and large values of PS, TPR, and PES; thus, suggesting that gene pairs identified by the SIG method are highly correlated with cancer progression, and highly enriched in disease-specific pathways. From

Pappas' scheme of correlating R6 and R4 co-ordinate transformations

International Nuclear Information System (INIS)

Teli, M.T.

1984-01-01

Pappas has suggested that R 4 co-ordinates can be connected with those in the R 6 by taking t'sub(x)=t'sub(y)=t'sub(z)=t'. Such connection is here obtained by introducing the scaling of space-time co-ordinates xsub(i), tsub(i) in all the frames by the corresponding factor c/c'sub(i) and have shown that taking of t'sub(x)=t'sub(y)=t'sub(z)=t' for this purpose is not necessary. The scaling factors get ignored after the connection

Gene expression responses of paper birch (Betula papyrifera) to elevated CO2 and O3 during leaf maturation and senescence

International Nuclear Information System (INIS)

Kontunen-Soppela, Sari; Parviainen, Juha; Ruhanen, Hanna; Brosche, Mikael; Keinaenen, Markku; Thakur, Ramesh C.; Kolehmainen, Mikko; Kangasjaervi, Jaakko; Oksanen, Elina; Karnosky, David F.; Vapaavuori, Elina

2010-01-01

Gene expression responses of paper birch (Betula papyrifera) leaves to elevated concentrations of CO 2 and O 3 were studied with microarray analyses from three time points during the summer of 2004 at Aspen FACE. Microarray data were analyzed with clustering techniques, self-organizing maps, K-means clustering and Sammon's mappings, to detect similar gene expression patterns within sampling times and treatments. Most of the alterations in gene expression were caused by O 3 , alone or in combination with CO 2 . O 3 induced defensive reactions to oxidative stress and earlier leaf senescence, seen as decreased expression of photosynthesis- and carbon fixation-related genes, and increased expression of senescence-associated genes. The effects of elevated CO 2 reflected surplus of carbon that was directed to synthesis of secondary compounds. The combined CO 2 + O 3 treatment resulted in differential gene expression than with individual gas treatments or in changes similar to O 3 treatment, indicating that CO 2 cannot totally alleviate the harmful effects of O 3 . - Clustering analysis of birch leaf gene expression data reveals differential responses to O 3 and CO 2 .

Co-ordinated research project on comparative international studies of osteoporosis using isotope techniques. Report on the final research co-ordination meeting

International Nuclear Information System (INIS)

2002-01-01

In 1994, the International Atomic Energy Agency started the five-year Co-ordinated Research Project (CRP) on Comparative International Studies of Osteoporosis Using Isotope Techniques. The objectives of this study were: To harmonize the techniques of measuring BMD within the participating countries and to obtain data that can be compared between the different study groups (countries); To determine whether early adult PBM varies between populations over the age range from 15 to 50 years. In other words, to determine the age of peak bone mass in selected populations from developing countries; To explore environmental and nutritional contributions to any determined differences. Further information about the purpose and scope of the CRP may be found in the report of the Advisory Group Meeting (AGM) held in 19921 and other reports of this CRP. The fourth Research Co-ordination Meeting (RCM) for participants of the CRP, which is the subject of the present report, was held at the University of Sheffield Medical School; WHO Collaborating Center for Metabolic Bone Diseases in Sheffield, UK from 28 Feb. to 3 March 2000

Co-ordination of physiological and morphological responses of stomata to elevated [CO2] in vascular plants.

Science.gov (United States)

Haworth, Matthew; Elliott-Kingston, Caroline; McElwain, Jennifer C

2013-01-01

Plant stomata display a wide range of short-term behavioural and long-term morphological responses to atmospheric carbon dioxide concentration ([CO(2)]). The diversity of responses suggests that plants may have different strategies for controlling gas exchange, yet it is not known whether these strategies are co-ordinated in some way. Here, we test the hypothesis that there is co-ordination of physiological (via aperture change) and morphological (via stomatal density change) control of gas exchange by plants. We examined the response of stomatal conductance (G(s)) to instantaneous changes in external [CO(2)] (C(a)) in an evolutionary cross-section of vascular plants grown in atmospheres of elevated [CO(2)] (1,500 ppm) and sub-ambient [O(2)] (13.0 %) compared to control conditions (380 ppm CO(2), 20.9 % O(2)). We found that active control of stomatal aperture to [CO(2)] above current ambient levels was not restricted to angiosperms, occurring in the gymnosperms Lepidozamia peroffskyana and Nageia nagi. The angiosperm species analysed appeared to possess a greater respiratory demand for stomatal movement than gymnosperm species displaying active stomatal control. Those species with little or no control of stomatal aperture (termed passive) to C(a) were more likely to exhibit a reduction in stomatal density than species with active stomatal control when grown in atmospheres of elevated [CO(2)]. The relationship between the degree of stomatal aperture control to C(a) above ambient and the extent of any reduction in stomatal density may suggest the co-ordination of physiological and morphological responses of stomata to [CO(2)] in the optimisation of water use efficiency. This trade-off between stomatal control strategies may have developed due to selective pressures exerted by the costs associated with passive and active stomatal control.

A gene co-expression network in whole blood of schizophrenia patients is independent of antipsychotic-use and enriched for brain-expressed genes.

Directory of Open Access Journals (Sweden)

Simone de Jong

Full Text Available Despite large-scale genome-wide association studies (GWAS, the underlying genes for schizophrenia are largely unknown. Additional approaches are therefore required to identify the genetic background of this disorder. Here we report findings from a large gene expression study in peripheral blood of schizophrenia patients and controls. We applied a systems biology approach to genome-wide expression data from whole blood of 92 medicated and 29 antipsychotic-free schizophrenia patients and 118 healthy controls. We show that gene expression profiling in whole blood can identify twelve large gene co-expression modules associated with schizophrenia. Several of these disease related modules are likely to reflect expression changes due to antipsychotic medication. However, two of the disease modules could be replicated in an independent second data set involving antipsychotic-free patients and controls. One of these robustly defined disease modules is significantly enriched with brain-expressed genes and with genetic variants that were implicated in a GWAS study, which could imply a causal role in schizophrenia etiology. The most highly connected intramodular hub gene in this module (ABCF1, is located in, and regulated by the major histocompatibility (MHC complex, which is intriguing in light of the fact that common allelic variants from the MHC region have been implicated in schizophrenia. This suggests that the MHC increases schizophrenia susceptibility via altered gene expression of regulatory genes in this network.

Roadside Judgments in Children with Developmental Co-ordination Disorder

Science.gov (United States)

Purcell, Catherine; Wann, John P.; Wilmut, Kate; Poulter, Damian

2011-01-01

As pedestrians, the perceptual ability to accurately judge the relative rate of approaching vehicles and select a suitable crossing gap requires sensitivity to looming. It also requires that crossing judgments are synchronized with motoric capabilities. Previous research has suggested that children with Developmental Co-ordination Disorder (DCD)…

Weighted gene co-expression network analysis of the peripheral blood from Amyotrophic Lateral Sclerosis patients

Directory of Open Access Journals (Sweden)

DeYoung Joseph

2009-08-01

Full Text Available Abstract Background Amyotrophic Lateral Sclerosis (ALS is a lethal disorder characterized by progressive degeneration of motor neurons in the brain and spinal cord. Diagnosis is mainly based on clinical symptoms, and there is currently no therapy to stop the disease or slow its progression. Since access to spinal cord tissue is not possible at disease onset, we investigated changes in gene expression profiles in whole blood of ALS patients. Results Our transcriptional study showed dramatic changes in blood of ALS patients; 2,300 probes (9.4% showed significant differential expression in a discovery dataset consisting of 30 ALS patients and 30 healthy controls. Weighted gene co-expression network analysis (WGCNA was used to find disease-related networks (modules and disease related hub genes. Two large co-expression modules were found to be associated with ALS. Our findings were replicated in a second (30 patients and 30 controls and third dataset (63 patients and 63 controls, thereby demonstrating a highly significant and consistent association of two large co-expression modules with ALS disease status. Ingenuity Pathway Analysis of the ALS related module genes implicates enrichment of functional categories related to genetic disorders, neurodegeneration of the nervous system and inflammatory disease. The ALS related modules contain a number of candidate genes possibly involved in pathogenesis of ALS. Conclusion This first large-scale blood gene expression study in ALS observed distinct patterns between cases and controls which may provide opportunities for biomarker development as well as new insights into the molecular mechanisms of the disease.

Co-ordinate expression of Th1/Th2 phenotypes in maternal and fetal blood: evidence for a transplacental nexus.

Science.gov (United States)

Tse, Doris B; Young, Bruce K

2012-01-06

If maternal atopy and environmental exposure affect prenatal Th cell development, the maternal and fetal immune systems should display common Th1/Th2 phenotypes. To test this hypothesis, we studied maternal and neonatal blood samples from mothers with total serum IgE ordinate IFN-γ production from paired maternal and fetal mononuclear cells, accompanied by co-ordinate increases in activated CD4+CD69+ cells that display the CCR4+Th2 and CXCR3+ Th1 phenotypes. Maternal and fetal CD4+CXCR3+ T cells were subsequently identified as the major producers of IFN-γ. The data established that a transplacental nexus exists during normal pregnancy and that fetal Th cell responses may be biased by the maternal immune system.

Effects of threshold on the topology of gene co-expression networks.

Science.gov (United States)

Couto, Cynthia Martins Villar; Comin, César Henrique; Costa, Luciano da Fontoura

2017-09-26

Several developments regarding the analysis of gene co-expression profiles using complex network theory have been reported recently. Such approaches usually start with the construction of an unweighted gene co-expression network, therefore requiring the selection of a suitable threshold defining which pairs of vertices will be connected. We aimed at addressing such an important problem by suggesting and comparing five different approaches for threshold selection. Each of the methods considers a respective biologically-motivated criterion for electing a potentially suitable threshold. A set of 21 microarray experiments from different biological groups was used to investigate the effect of applying the five proposed criteria to several biological situations. For each experiment, we used the Pearson correlation coefficient to measure the relationship between each gene pair, and the resulting weight matrices were thresholded considering several values, generating respective adjacency matrices (co-expression networks). Each of the five proposed criteria was then applied in order to select the respective threshold value. The effects of these thresholding approaches on the topology of the resulting networks were compared by using several measurements, and we verified that, depending on the database, the impact on the topological properties can be large. However, a group of databases was verified to be similarly affected by most of the considered criteria. Based on such results, it can be suggested that when the generated networks present similar measurements, the thresholding method can be chosen with greater freedom. If the generated networks are markedly different, the thresholding method that better suits the interests of each specific research study represents a reasonable choice.

Gene co-expression networks shed light into diseases of brain iron accumulation.

Science.gov (United States)

Bettencourt, Conceição; Forabosco, Paola; Wiethoff, Sarah; Heidari, Moones; Johnstone, Daniel M; Botía, Juan A; Collingwood, Joanna F; Hardy, John; Milward, Elizabeth A; Ryten, Mina; Houlden, Henry

2016-03-01

Aberrant brain iron deposition is observed in both common and rare neurodegenerative disorders, including those categorized as Neurodegeneration with Brain Iron Accumulation (NBIA), which are characterized by focal iron accumulation in the basal ganglia. Two NBIA genes are directly involved in iron metabolism, but whether other NBIA-related genes also regulate iron homeostasis in the human brain, and whether aberrant iron deposition contributes to neurodegenerative processes remains largely unknown. This study aims to expand our understanding of these iron overload diseases and identify relationships between known NBIA genes and their main interacting partners by using a systems biology approach. We used whole-transcriptome gene expression data from human brain samples originating from 101 neuropathologically normal individuals (10 brain regions) to generate weighted gene co-expression networks and cluster the 10 known NBIA genes in an unsupervised manner. We investigated NBIA-enriched networks for relevant cell types and pathways, and whether they are disrupted by iron loading in NBIA diseased tissue and in an in vivo mouse model. We identified two basal ganglia gene co-expression modules significantly enriched for NBIA genes, which resemble neuronal and oligodendrocytic signatures. These NBIA gene networks are enriched for iron-related genes, and implicate synapse and lipid metabolism related pathways. Our data also indicates that these networks are disrupted by excessive brain iron loading. We identified multiple cell types in the origin of NBIA disorders. We also found unforeseen links between NBIA networks and iron-related processes, and demonstrate convergent pathways connecting NBIAs and phenotypically overlapping diseases. Our results are of further relevance for these diseases by providing candidates for new causative genes and possible points for therapeutic intervention. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Feasibility of central co-ordinated EMA/CO for gestational trophoblastic disease in the Netherlands

NARCIS (Netherlands)

van der Houwen, Clasien; Rietbroek, Ron C.; Lok, Christianne A. R.; ten Kate-Booij, Marianne J.; Lammes, Frits B.; Ansink, Anca C.

2004-01-01

In the Netherlands, high risk gestational trophoblastic disease (GTD) patients are treated in different referral hospitals with a national working party on trophoblastic tumours having a co-ordinating function. Our purpose was to evaluate whether this policy is a satisfactory alternative to complete

Different gene expression of Normal lymphobloastoid cells which exposure to different dose of 60Co γ-ray

International Nuclear Information System (INIS)

Xiao Yao; Yang Jian; Gao Xian; Qin Yanghua; Sun Ding; Hai Ling

2008-01-01

Objective: To study on the gene expression of normal lymphoblastoid cells(AHH-1) which exposure to difference dose of 60 Co γ-ray, analyses the essential different biological effect.. Methods Human AHH-1 normal line was irradiated by 60 Co γ-rays. Used human cDNA microarray to develop the transcriptional levels of the genes by hybridizing the mRNA of cells 8 h after exposured in different dose and the control cells. Cluster analysis, discrimination and bolting were used to filter the effective genes of differential expression. Results The results of data analysis showed 23 genes of differential expression closely related to biological effect of 2.0 Gy radiation, 5 genes express changed only by 0.5 Gy radiation, 5 genes express apparently both in 2.0 Gy and 0.5 Gy radiation. Conclusion: The different dose γ-rays radiation-induced significant changes in gene expression, such as PAPLN, TP53INP1, PTENP1, FOS and TPR seem to be some important components of cellular radioresponse. (authors)

Supply chain co-ordination and industry clockspeed: an exploratory study

NARCIS (Netherlands)

Voordijk, Johannes T.; Akkermans, Henk; Meijboom, Bert

2003-01-01

The increasing velocity of change, or clockspeed, in the business environment is a key challenge for firms and industries nowadays. In this study, the impact of industry and organisation clockspeed on specific mechanisms used for supply chain co-ordination is investigated from an

Rain Scattering and Co-ordinate Distance Calculation

Directory of Open Access Journals (Sweden)

M. Hajny

1998-12-01

Full Text Available Calculations of scattered field on the rain objects are based on using of Multiple MultiPole (MMP numerical method. Both bi-static scattering function and bi-static scattering cross section are calculated in the plane parallel to Earth surface. The co-ordination area was determined using the simple model of scattering volume [1]. Calculation for frequency 9.595 GHz and antenna elevation of 25° was done. Obtained results are compared with calculation in accordance to ITU-R recommendation.

On Constancy of Second Co-ordinate of the gonality sequence

OpenAIRE

Pal, Sarbeswar

2017-01-01

Let $X$ be a K3 surface and $L$ be an ample line bundle on it. In this article we will prove that under certain condition the second co-ordinate of the gonality sequence is constant along the smooth curves in the linear system $|L|$.

Co-Cultures of Pseudomonas aeruginosa and Roseobacter denitrificans Reveal Shifts in Gene Expression Levels Compared to Solo Cultures

Directory of Open Access Journals (Sweden)

Crystal A. Conway

2012-01-01

Full Text Available Consistent biosynthesis of desired secondary metabolites (SMs from pure microbial cultures is often unreliable. In a proof-of-principle study to induce SM gene expression and production, we describe mixed “co-culturing” conditions and monitoring of messages via quantitative real-time PCR (qPCR. Gene expression of model bacterial strains (Pseudomonas aeruginosa PAO1 and Roseobacter denitrificans Och114 was analyzed in pure solo and mixed cocultures to infer the effects of interspecies interactions on gene expression in vitro, Two P. aeruginosa genes (PhzH coding for portions of the phenazine antibiotic pathway leading to pyocyanin (PCN and the RhdA gene for thiosulfate: cyanide sulfurtransferase (Rhodanese and two R. denitrificans genes (BetaLact for metallo-beta-lactamase and the DMSP gene for dimethylpropiothetin dethiomethylase were assessed for differential expression. Results showed that R. denitrificans DMSP and BetaLact gene expression became elevated in a mixed culture. In contrast, P. aeruginosa co-cultures with R. denitrificans or a third species did not increase target gene expression above control levels. This paper provides insight for better control of target SM gene expression in vitro and bypass complex genetic engineering manipulations.

Preparation and crystal structure of carbonyltris (diethyldithiocarbamato) technetium (III): an unexpected source of co-ordinated carbon monoxide

International Nuclear Information System (INIS)

Baldas, J.; Bonnyman, J.; Pojer, P.M.; Williams, G.A.

1981-10-01

Tc(S 2 CNEt 2 ) 3 CO has been prepared by the reduction of NH 4 TcO 4 with formamidinesulphinic acid in the presence of NaS 2 CNEt 2 . It is suggested that the co-ordinated carbon monoxide is formed after co-ordination of formamidinesulphinic acid, or some decomposition product, with technetium. The crystal structure of Tc(S 2 CNEt 2 ) 3 CO has been determined by single-crystal X-ray diffraction methods at 17 deg. C. Diffractometry has provided significant Bragg intensities for 2045 independent reflections and the structure has been refined by full-matrix least-squares methods to R 0.049. The compound is isostructural with the rhenium analogue and consists of discrete Tc(S 2 CNEt 2 ) 3 CO molecules, each containing a terminal linear CO group. The technetium atom has a seven co-ordinate environment which is best described as a distorted pentagonal bipyramid

Analysis of the morphology of oral structures from 3-D co-ordinate data.

Science.gov (United States)

Jovanovski, V; Lynch, E

2000-01-01

A non-intrusive method is described which can be used to determine the forms of oral structures. It is based on the digitising of standard replicas with a co-ordinate-measuring machine. Supporting software permits a mathematical model of the surface to be reconstructed and visualised from captured three-dimensional co-ordinates. A series of surface data sets can be superposed into a common reference frame without the use of extrinsic markers, allowing changes in the shapes of oral structures to be quantified accurately over an extended period of time. The system has found numerous applications.

Co-ordinated research programme on isotope-aided studies of the bioavailability of iron and zinc from human diets. Report of the second research co-ordination meeting, Hyderabad, India, 16-20 November 1992

International Nuclear Information System (INIS)

1994-01-01

The Co-ordinated Research Programme (CRP) on ''Isotope-Aided Studies on the Bioavailability of Iron and Zinc from Human Diets'' was initiated by the IAEA in 1990, and presently encompasses participating institutes in 11 countries. A summary of the discussions that took place during thr second Research Co-ordination Meeting held in Hyderabad, India, between 16-20 November 1992, is given in this report together with 12 working papers (progress reports) presented by individual participants. A separate abstract was prepared for each of these papers. Refs, figs and tabs

Genes and co-expression modules common to drought and bacterial stress responses in Arabidopsis and rice.

Directory of Open Access Journals (Sweden)

Rafi Shaik

Full Text Available Plants are simultaneously exposed to multiple stresses resulting in enormous changes in the molecular landscape within the cell. Identification and characterization of the synergistic and antagonistic components of stress response mechanisms contributing to the cross talk between stresses is of high priority to explore and enhance multiple stress responses. To this end, we performed meta-analysis of drought (abiotic, bacterial (biotic stress response in rice and Arabidopsis by analyzing a total of 386 microarray samples belonging to 20 microarray studies and identified approximately 3100 and 900 DEGs in rice and Arabidopsis, respectively. About 38.5% (1214 and 28.7% (272 DEGs were common to drought and bacterial stresses in rice and Arabidopsis, respectively. A majority of these common DEGs showed conserved expression status in both stresses. Gene ontology enrichment analysis clearly demarcated the response and regulation of various plant hormones and related biological processes. Fatty acid metabolism and biosynthesis of alkaloids were upregulated and, nitrogen metabolism and photosynthesis was downregulated in both stress conditions. WRKY transcription family genes were highly enriched in all upregulated gene sets while 'CO-like' TF family showed inverse relationship of expression between drought and bacterial stresses. Weighted gene co-expression network analysis divided DEG sets into multiple modules that show high co-expression and identified stress specific hub genes with high connectivity. Detection of consensus modules based on DEGs common to drought and bacterial stress revealed 9 and 4 modules in rice and Arabidopsis, respectively, with conserved and reversed co-expression patterns.

Overcurrent protection co-ordination. A modern approach for modern devices

Energy Technology Data Exchange (ETDEWEB)

Hindle, P. [GEC Alsthom Engineering Systems Ltd., Whetstone (United Kingdom); Sanderson, J.V.H. [Power Engineering Consultants Ltd., Cheshire (United Kingdom)

1995-12-31

A modern approach to relay co-ordination that takes advantage of the improved performance of modern protective relays and circuits was proposed. The proposed method dealt with a mixture of new and old equipment and was most useful when implemented using common spreadsheet software. The suggested approach justified reduced time margins for relay co-ordination in many difficult applications. Other established approaches were reviewed. A discussion of fixed and variable time margin allowances was presented. The formulation of an equation to determine the required upstream relay operating time was explained, with sample calculations. Relay performance standards and modern protective equipment were discussed. It was concluded that modern relays and circuit breakers are much more advanced than designs of the recent past. The method described allowed significant reductions in margins which enabled modern relays to operate faster. While calculations for the procedures were said to be tedious to perform by hand, they can be easily done with spreadsheet software. 10 refs., 4 figs.

Gene co-expression analysis identifies gene clusters associated with isotropic and polarized growth in Aspergillus fumigatus conidia.

Science.gov (United States)

Baltussen, Tim J H; Coolen, Jordy P M; Zoll, Jan; Verweij, Paul E; Melchers, Willem J G

2018-04-26

Aspergillus fumigatus is a saprophytic fungus that extensively produces conidia. These microscopic asexually reproductive structures are small enough to reach the lungs. Germination of conidia followed by hyphal growth inside human lungs is a key step in the establishment of infection in immunocompromised patients. RNA-Seq was used to analyze the transcriptome of dormant and germinating A. fumigatus conidia. Construction of a gene co-expression network revealed four gene clusters (modules) correlated with a growth phase (dormant, isotropic growth, polarized growth). Transcripts levels of genes encoding for secondary metabolites were high in dormant conidia. During isotropic growth, transcript levels of genes involved in cell wall modifications increased. Two modules encoding for growth and cell cycle/DNA processing were associated with polarized growth. In addition, the co-expression network was used to identify highly connected intermodular hub genes. These genes may have a pivotal role in the respective module and could therefore be compelling therapeutic targets. Generally, cell wall remodeling is an important process during isotropic and polarized growth, characterized by an increase of transcripts coding for hyphal growth and cell cycle/DNA processing when polarized growth is initiated. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Improvement of basic food crops in Africa through plant breeding, including the use of induced mutations. Report of the third research co-ordination meeting of FAO/IAEA/ITALY co-ordinated research programme. Working material

Energy Technology Data Exchange (ETDEWEB)

NONE

1997-12-01

A Co-ordinated Research Programme, on ``Improvement of basic food corps in Africa through plant breeding including the use of induced mutations``, funded by the Italian Governmnet, was initiated in the Joint Division of the Food and Agriculture Organization and International Atomic Energy Agency, Vienna. The primary objective of this CRP was to breed improved varieties of staple food crops of Africa with main emphasis on the indigenous species and local cultivars. The Third Research Co-ordination Meeting (RCM) under the FAO/IAEA/ITALY Co-ordinated Research Programme was held in Nairobi, Kenya, 20-24 September 1993 in which 24 persons participated and 18 scientific reports were presented. These included reports from 10 Research Contract holders from Africa, 3 Technical Contract holders from Italy and the update on the backstopping of research carried out at the IAEA Laboratories, Seibersdorf. The reports, and conclusions and recommendations made by the participants are presented in this publication. Refs, figs, tabs.

Improvement of basic food crops in Africa through plant breeding, including the use of induced mutations. Report of the third research co-ordination meeting of FAO/IAEA/ITALY co-ordinated research programme. Working material

International Nuclear Information System (INIS)

1997-01-01

A Co-ordinated Research Programme, on ''Improvement of basic food corps in Africa through plant breeding including the use of induced mutations'', funded by the Italian Governmnet, was initiated in the Joint Division of the Food and Agriculture Organization and International Atomic Energy Agency, Vienna. The primary objective of this CRP was to breed improved varieties of staple food crops of Africa with main emphasis on the indigenous species and local cultivars. The Third Research Co-ordination Meeting (RCM) under the FAO/IAEA/ITALY Co-ordinated Research Programme was held in Nairobi, Kenya, 20-24 September 1993 in which 24 persons participated and 18 scientific reports were presented. These included reports from 10 Research Contract holders from Africa, 3 Technical Contract holders from Italy and the update on the backstopping of research carried out at the IAEA Laboratories, Seibersdorf. The reports, and conclusions and recommendations made by the participants are presented in this publication. Refs, figs, tabs

Co-ordinating innate and adaptive immunity to viral infection: mobility is the key

DEFF Research Database (Denmark)

Wern, Jeanette Erbo; Thomsen, Allan Randrup

2009-01-01

The host counters a viral infection through a complex response made up of components belonging to both the innate and the adaptive immune system. In this report, we review the mechanisms underlying this response, how it is induced and how it is co-ordinated. As cell-cell communication represents...... the very essence of immune system physiology, a key to a rapid, efficient and optimally regulated immune response is the ability of the involved cells to rapidly shift between a stationary and a mobile state, combined with stringent regulation of cell migration during the mobile state. Through the co......-ordinated recruitment of different cell types intended to work in concert, cellular co-operation is optimized particularly under conditions that may involve rare cells. Consequently, a major focus is placed on presenting an overview of the co-operative events and the associated cell migration, which is essential...

The functional landscape of mouse gene expression

Directory of Open Access Journals (Sweden)

Zhang Wen

2004-12-01

Full Text Available Abstract Background Large-scale quantitative analysis of transcriptional co-expression has been used to dissect regulatory networks and to predict the functions of new genes discovered by genome sequencing in model organisms such as yeast. Although the idea that tissue-specific expression is indicative of gene function in mammals is widely accepted, it has not been objectively tested nor compared with the related but distinct strategy of correlating gene co-expression as a means to predict gene function. Results We generated microarray expression data for nearly 40,000 known and predicted mRNAs in 55 mouse tissues, using custom-built oligonucleotide arrays. We show that quantitative transcriptional co-expression is a powerful predictor of gene function. Hundreds of functional categories, as defined by Gene Ontology 'Biological Processes', are associated with characteristic expression patterns across all tissues, including categories that bear no overt relationship to the tissue of origin. In contrast, simple tissue-specific restriction of expression is a poor predictor of which genes are in which functional categories. As an example, the highly conserved mouse gene PWP1 is widely expressed across different tissues but is co-expressed with many RNA-processing genes; we show that the uncharacterized yeast homolog of PWP1 is required for rRNA biogenesis. Conclusions We conclude that 'functional genomics' strategies based on quantitative transcriptional co-expression will be as fruitful in mammals as they have been in simpler organisms, and that transcriptional control of mammalian physiology is more modular than is generally appreciated. Our data and analyses provide a public resource for mammalian functional genomics.

An additional k-means clustering step improves the biological features of WGCNA gene co-expression networks.

Science.gov (United States)

Botía, Juan A; Vandrovcova, Jana; Forabosco, Paola; Guelfi, Sebastian; D'Sa, Karishma; Hardy, John; Lewis, Cathryn M; Ryten, Mina; Weale, Michael E

2017-04-12

Weighted Gene Co-expression Network Analysis (WGCNA) is a widely used R software package for the generation of gene co-expression networks (GCN). WGCNA generates both a GCN and a derived partitioning of clusters of genes (modules). We propose k-means clustering as an additional processing step to conventional WGCNA, which we have implemented in the R package km2gcn (k-means to gene co-expression network, https://github.com/juanbot/km2gcn ). We assessed our method on networks created from UKBEC data (10 different human brain tissues), on networks created from GTEx data (42 human tissues, including 13 brain tissues), and on simulated networks derived from GTEx data. We observed substantially improved module properties, including: (1) few or zero misplaced genes; (2) increased counts of replicable clusters in alternate tissues (x3.1 on average); (3) improved enrichment of Gene Ontology terms (seen in 48/52 GCNs) (4) improved cell type enrichment signals (seen in 21/23 brain GCNs); and (5) more accurate partitions in simulated data according to a range of similarity indices. The results obtained from our investigations indicate that our k-means method, applied as an adjunct to standard WGCNA, results in better network partitions. These improved partitions enable more fruitful downstream analyses, as gene modules are more biologically meaningful.

The use of the co-ordinate measuring machine for the study of three-dimensional biomechanics of the knee.

Science.gov (United States)

Veselko, M; Jenko, M; Lipuscek, I

1998-07-01

Original methodology for the study of three-dimensional biomechanics of the knee is presented in the paper. Defining the geometry of the rigid body in the body-fixed reference frame and the orientation of the body-fixed reference frame in the global co-ordinate system are the theoretic basis. The data in the form of co-ordinates of the Cartesian frame are gathered by the co-ordinate measuring machine and analysed by specially computer program. The theory and a practical example of the study of the three-dimensional biomechanics of the knee are presented. Various possibilities of the use of the methodology are discussed.

Prediction of operon-like gene clusters in the Arabidopsis thaliana genome based on co-expression analysis of neighboring genes.

Science.gov (United States)

Wada, Masayoshi; Takahashi, Hiroki; Altaf-Ul-Amin, Md; Nakamura, Kensuke; Hirai, Masami Y; Ohta, Daisaku; Kanaya, Shigehiko

2012-07-15

Operon-like arrangements of genes occur in eukaryotes ranging from yeasts and filamentous fungi to nematodes, plants, and mammals. In plants, several examples of operon-like gene clusters involved in metabolic pathways have recently been characterized, e.g. the cyclic hydroxamic acid pathways in maize, the avenacin biosynthesis gene clusters in oat, the thalianol pathway in Arabidopsis thaliana, and the diterpenoid momilactone cluster in rice. Such operon-like gene clusters are defined by their co-regulation or neighboring positions within immediate vicinity of chromosomal regions. A comprehensive analysis of the expression of neighboring genes therefore accounts a crucial step to reveal the complete set of operon-like gene clusters within a genome. Genome-wide prediction of operon-like gene clusters should contribute to functional annotation efforts and provide novel insight into evolutionary aspects acquiring certain biological functions as well. We predicted co-expressed gene clusters by comparing the Pearson correlation coefficient of neighboring genes and randomly selected gene pairs, based on a statistical method that takes false discovery rate (FDR) into consideration for 1469 microarray gene expression datasets of A. thaliana. We estimated that A. thaliana contains 100 operon-like gene clusters in total. We predicted 34 statistically significant gene clusters consisting of 3 to 22 genes each, based on a stringent FDR threshold of 0.1. Functional relationships among genes in individual clusters were estimated by sequence similarity and functional annotation of genes. Duplicated gene pairs (determined based on BLAST with a cutoff of EOperon-like clusters tend to include genes encoding bio-machinery associated with ribosomes, the ubiquitin/proteasome system, secondary metabolic pathways, lipid and fatty-acid metabolism, and the lipid transfer system. Copyright © 2012 Elsevier B.V. All rights reserved.

Rigid Body Motion Calculated From Spatial Co-ordinates of Markers ...

African Journals Online (AJOL)

In this paper, we present a unified method for calculating spatial coordinates of markers for a rigid body motion such as in bones. Kinematical analysis of bone movement in cadaveric specimens or living objects had been developed. Here, we show how spatial co-ordinates of markers in or on bone can be calculated from ...

Weighted gene co-expression network analysis reveals potential genes involved in early metamorphosis process in sea cucumber Apostichopus japonicus.

Science.gov (United States)

Li, Yongxin; Kikuchi, Mani; Li, Xueyan; Gao, Qionghua; Xiong, Zijun; Ren, Yandong; Zhao, Ruoping; Mao, Bingyu; Kondo, Mariko; Irie, Naoki; Wang, Wen

2018-01-01

Sea cucumbers, one main class of Echinoderms, have a very fast and drastic metamorphosis process during their development. However, the molecular basis under this process remains largely unknown. Here we systematically examined the gene expression profiles of Japanese common sea cucumber (Apostichopus japonicus) for the first time by RNA sequencing across 16 developmental time points from fertilized egg to juvenile stage. Based on the weighted gene co-expression network analysis (WGCNA), we identified 21 modules. Among them, MEdarkmagenta was highly expressed and correlated with the early metamorphosis process from late auricularia to doliolaria larva. Furthermore, gene enrichment and differentially expressed gene analysis identified several genes in the module that may play key roles in the metamorphosis process. Our results not only provide a molecular basis for experimentally studying the development and morphological complexity of sea cucumber, but also lay a foundation for improving its emergence rate. Copyright © 2017 Elsevier Inc. All rights reserved.

Co-ordinate single-cell expression of LEE4- and LEE5-encoded proteins of Escherichia coli O157:H7.

Science.gov (United States)

Roe, Andrew J; Naylor, Stuart W; Spears, Kevin J; Yull, Helen M; Dransfield, Tracy A; Oxford, Matthew; McKendrick, Iain J; Porter, Megan; Woodward, Martin J; Smith, David G E; Gally, David L

2004-10-01

Escherichia coli O157:H7 is a zoonotic pathogen that can express a type III secretion system (TTSS) considered important for colonization and persistence in ruminants. E. coli O157:H7 strains have been shown to vary markedly in levels of protein secreted using the TTSS and this study has confirmed that a high secretion phenotype is more prevalent among isolates associated with human disease than isolates shed by healthy cattle. The variation in secretion levels is a consequence of heterogeneous expression, being dependent on the proportion of bacteria in a population that are actively engaged in protein secretion. This was demonstrated by indirect immunofluorescence and eGFP fusions that examined the expression of locus of enterocyte effacement (LEE)-encoded factors in individual bacteria. In liquid media, the expression of EspA, tir::egfp, intimin, but not map::egfp were co-ordinated in a subpopulation of bacteria. In contrast to E. coli O157:H7, expression of tir::egfp in EPEC E2348/69 was equivalent in all bacteria although the same fusion exhibited variable expression when transformed into an E. coli O157:H7 background. An E. coli O157:H7 strain deleted for the LEE demonstrated weak but variable expression of tir::egfp indicating that the elements controlling the heterogeneous expression lie outside the LEE. The research also demonstrated the rapid induction of tir::egfp and map::egfp on contact with bovine epithelial cells. This control in E. coli O157:H7 may be required to limit exposure of key surface antigens, EspA, Tir and intimin during colonization of cattle but allow their rapid production on contact with bovine gastrointestinal epithelium at the terminal rectum.

Co-ordinated traffic control in freeway corridors : A proposed evaluation approach

NARCIS (Netherlands)

Hoogendoorn, S.P.; Bovy, P.H.L.; Van der Zijpp, N.J.

1997-01-01

In the course of the Telematics implications Programme Transport of the European Commission Fourth Framework Research Programme much attention is devoted to evaluation and demonstration. This report is part of the DACCORD project TR1017, devoted to the development and application of co-ordinated

Effect of co-culture with enterocinogenic E. faecium on L. monocytogenes key virulence gene expression

Directory of Open Access Journals (Sweden)

Eleftherios H. Drosinos

2016-08-01

Full Text Available The aim of the present study was to assess the expression of key virulence genes during co-culture of L. monocytogenes with a bacteriocinogenic E. faecium strain in liquid growth medium. For that purpose, BHI broth was inoculated with 7 log CFU·mL–1 L. monocytogenes and 4, 5 or 6 log CFU·mL–1 E. faecium. Sampling took place after 8 and 24 h of incubation, corresponding to the maximum and minimum of enterocin production, respectively. The RNA was extracted, stabilized and expression of prfA, sigB, hly, plcA, plcB, inlA, inlB, inlC and inlJ, was assessed by RT-qPCR. Most of the genes were downregulated during co-culture at 5 °C. Moreover, a statistically significant effect of the inoculum level was evident in most of the cases. On the contrary, no effect on the transcription level of most of the genes was observed during co-culture at 37 °C.

Cross-organisational workflow management and co-ordination: WACC'99 workshop report

NARCIS (Netherlands)

Ludwig, Heiko; Bussler, Christoph; Shan, Ming-Chien; Grefen, P.W.P.J.

The increasing deployment of Workflow Management Systems (WfMSs) and other co-ordination and process support systems on the one hand and the proliferation of cheap networking, namely the Internet, on the other hand raises the issue of how to connect these systems across organisational boundaries.

Changing Housing for Elderly People and Co-ordination Issues in Europe

NARCIS (Netherlands)

Houben, P.P.J.A.M.

2001-01-01

The inter-sectoral policy systems of housing for elderly people in the EU-countries change with the implementation of ageing in place and by general processes of modernisation of society and welfare state. For implementation of the innovations the relevance of co-ordination between the sector

A co-expression gene network associated with developmental regulation of apple fruit acidity.

Science.gov (United States)

Bai, Yang; Dougherty, Laura; Cheng, Lailiang; Xu, Kenong

2015-08-01

Apple fruit acidity, which affects the fruit's overall taste and flavor to a large extent, is primarily determined by the concentration of malic acid. Previous studies demonstrated that the major QTL malic acid (Ma) on chromosome 16 is largely responsible for fruit acidity variations in apple. Recent advances suggested that a natural mutation that gives rise to a premature stop codon in one of the two aluminum-activated malate transporter (ALMT)-like genes (called Ma1) is the genetic causal element underlying Ma. However, the natural mutation does not explain the developmental changes of fruit malate levels in a given genotype. Using RNA-seq data from the fruit of 'Golden Delicious' taken at 14 developmental stages from 1 week after full-bloom (WAF01) to harvest (WAF20), we characterized their transcriptomes in groups of high (12.2 ± 1.6 mg/g fw, WAF03-WAF08), mid (7.4 ± 0.5 mg/g fw, WAF01-WAF02 and WAF10-WAF14) and low (5.4 ± 0.4 mg/g fw, WAF16-WAF20) malate concentrations. Detailed analyses showed that a set of 3,066 genes (including Ma1) were expressed not only differentially (P FDR < 0.05) between the high and low malate groups (or between the early and late developmental stages) but also in significant (P < 0.05) correlation with malate concentrations. The 3,066 genes fell in 648 MapMan (sub-) bins or functional classes, and 19 of them were significantly (P FDR < 0.05) co-enriched or co-suppressed in a malate dependent manner. Network inferring using the 363 genes encompassed in the 19 (sub-) bins, identified a major co-expression network of 239 genes. Since the 239 genes were also differentially expressed between the early (WAF03-WAF08) and late (WAF16-WAF20) developmental stages, the major network was considered to be associated with developmental regulation of apple fruit acidity in 'Golden Delicious'.

Rice breeding with induced mutations II. Report of an FAO/IAEA research co-ordination meeting

Energy Technology Data Exchange (ETDEWEB)

NONE

1970-03-01

This report contains the proceedings of the fourth meeting of participants in the FAO/IAEA Co-ordinated Program of Research on the Use of Induced Mutations in Rice Breeding, a program which was initiated in 1964. The three previous meetings were reported as follows: First: proceedings published in the International Rice Commission Newsletter, Vol. XV, No. 1 (1966). Second: report presented to the IRC Working Party meeting at Lake Charles, Louisiana, 18-30 July 1966. Third: proceedings published by the IAEA as Technical Reports Series No. 86 under the title 'Rice breeding with induced mutations'. The fourth meeting was held at Oiso, Japan, on 12-14 August 1968. Co-operators from nine countries attended, together with scientists from five other countries, the International Rice Research Institute, the Rockefeller Foundation, the International Rice Commission, and the FAO and IAEA. In addition, a number of scientists from the host country were present. The purpose of the meeting was to present reports on research related to or carried out under the co-ordinated program in 1967/68, to review and co-ordinate research plans for 1968/69, and to draw up technical recommendations for future work.

Cloning and expression analysis of cinnamoyl-CoA reductase (CCR) genes in sorghum.

Science.gov (United States)

Li, Jieqin; Fan, Feifei; Wang, Lihua; Zhan, Qiuwen; Wu, Peijin; Du, Junli; Yang, Xiaocui; Liu, Yanlong

2016-01-01

Cinnamoyl-CoA reductase (CCR) is the first enzyme in the monolignol-specific branch of the lignin biosynthetic pathway. In this research, three sorghum CCR genes including SbCCR1, SbCCR2-1 and SbCCR2-2 were cloned and characterized. Analyses of the structure and phylogeny of the three CCR genes showed evolutionary conservation of the functional domains and divergence of function. Transient expression assays in Nicotiana benthamiana leaves demonstrated that the three CCR proteins were localized in the cytoplasm. The expression analysis showed that the three CCR genes were induced by drought. But in 48 h, the expression levels of SbCCR1 and SbCCR2-2 did not differ between CK and the drought treatment; while the expression level of SbCCR2-1 in the drought treatment was higher than in CK. The expression of the SbCCR1 and SbCCR2-1 genes was not induced by sorghum aphid [Melanaphis sacchari (Zehntner)] attack, but SbCCR2-2 was significantly induced by sorghum aphid attack. It is suggested that SbCCR2-2 is involved in the process of pest defense. Absolute quantitative real-time PCR revealed that the three CCR genes were mainly expressed in lignin deposition organs. The gene copy number of SbCCR1 was significantly higher than those of SbCCR2-1 and SbCCR2-2 in the tested tissues, especially in stem. The results provide new insight into the functions of the three CCR genes in sorghum.

Divalent cations and the protein surface co-ordinate the intensity of human platelet adhesion and P-selectin surface expression.

Science.gov (United States)

Whiss, P A; Andersson, R G G

2002-07-01

At sites of blood vessel injury, platelets adhere to exposed vessel components, such as collagen, or immobilized fibrinogen derived from plasma or activated platelets. The divalent cations Mg(2+) and Ca(2+) are essential for platelet adhesion and activation, but Mg(2+) can also inhibit platelet activation. The present study evaluates, by an enzymatic method, the effects of various divalent cations on the adhesion of isolated human platelets to collagen, fibrinogen, albumin or plastic in vitro. By enzyme-linked immunosorbent assay, platelet surface expression of P-selectin was measured to estimate the state of activation on adherence. Mg(2+) increased platelet adhesion exclusively to collagen and fibrinogen at physiologically relevant concentrations. At higher concentrations, the adhesion declined. Ca(2+) induced a weak adhesion only to fibrinogen at physiological doses and a peak of increased adhesion to all protein-coated surfaces at 10 mmol/l. Mn(2+) elicited dose-dependent adhesion only to collagen and fibrinogen. Zn(2+), Ni(2+) and Cu(2+) increased the adhesion of platelets independently of the surface. Ca(2+) dose-dependently inhibited adhesion elicited by Mg(2+) to collagen and fibrinogen. No other combination of divalent cations elicited such an effect. Mg(2+)-dependent platelet adhesion to collagen and Ca(2+)-dependent adhesion to fibrinogen increased P-selectin expression. Thus, the present study shows that the outcome of the platelet adhesion depends on the surface and the access of divalent cations, which co-ordinate the intensity of platelet adhesion and P-selectin surface expression.

The Standards Agenda: Reflections of a Special Educational Needs Co-ordinator

Science.gov (United States)

Glazzard, Jonathan

2014-01-01

This study is a life history account of Bev, a special educational needs co-ordinator who works in a primary school in England. The research examines how, within Bev's experiences, the discourses of integration and inclusion have affected learners with special educational needs. Additionally, the study examines the impact of the…

, , , , , and Gene Expression in Single- and Co-cultured Bovine Satellite Cells and Intramuscular Preadipocytes Treated with Palmitic, Stearic, Oleic, and Linoleic Acid

Directory of Open Access Journals (Sweden)

S. H. Choi

2015-03-01

Full Text Available We previously demonstrated that bovine subcutaneous preadipocytes promote adipogenic gene expression in muscle satellite cells in a co-culture system. Herein we hypothesize that saturated fatty acids would promote adipogenic/lipogenic gene expression, whereas mono- and polyunsaturated fatty acids would have the opposite effect. Bovine semimembranosus satellite cells (BSC and intramuscular preadipocytes (IPA were isolated from crossbred steers and cultured with 10% fetal bovine serum (FBS/Dulbecco’s Modified Eagle Medium (DMEM and 1% antibiotics during the 3-d proliferation period. After proliferation, cells were treated for 3 d with 3% horse serum/DMEM (BSC or 5% FBS/DMEM (IPA with antibiotics. Media also contained 10 μg/mL insulin and 10 μg/mL pioglitazone. Subsequently, differentiating BSC and IPA were cultured in their respective media with 40 μM palmitic, stearic, oleic, or linoleic acid for 4 d. Finally, BSC and IPA were single- or co-cultured for an additional 2 h. All fatty acid treatments increased (p = 0.001 carnitine palmitoyltransferase-1 beta (CPT1β gene expression, but the increase in CPT1β gene expression was especially pronounced in IPA incubated with palmitic and stearic acid (6- to 17- fold increases. Oleic and linoleic acid decreased (p = 0.001 stearoyl-CoA desaturase (SCD gene expression over 80% in both BSC and IPA. Conversely, palmitic and stearic acid increased SCD gene expression three fold in co-cultured in IPA, and stearic acid increased AMPKα gene expression in single- and co-cultured BSC and IPA. Consistent with our hypothesis, saturated fatty acids, especially stearic acid, promoted adipogenic and lipogenic gene expression, whereas unsaturated fatty acids decreased expression of those genes associated with fatty acid metabolism.

The relationship between temperamental traits and the level of performance of an eye-hand co-ordination task in jet pilots.

Science.gov (United States)

Biernacki, Marcin; Tarnowski, Adam

2008-01-01

When assessing the psychological suitability for the profession of a pilot, it is important to consider personality traits and psychomotor abilities. Our study aimed at estimating the role of temperamental traits as components of pilots' personality in eye-hand co-ordination. The assumption was that differences in the escalation of the level of temperamental traits, as measured with the Formal Characteristic of Behaviour-Temperament Inventory (FCB-TI), will significantly influence eye-hand co-ordination. At the level of general scores, enhanced briskness proved to be the most important trait for eye-hand co-ordination. An analysis of partial scores additionally underlined the importance of sensory sensitivity, endurance and activity. The application of eye-hand co-ordination tasks, which involve energetic and temporal dimensions of performance, helped to disclose the role of biologically-based personality traits in psychomotor performance. The implication of these findings for selecting pilots is discussed.

A contribution to the study of plant development evolution based on gene co-expression networks

Directory of Open Access Journals (Sweden)

Francisco J. Romero-Campero

2013-08-01

Full Text Available Phototrophic eukaryotes are among the most successful organisms on Earth due to their unparalleled efficiency at capturing light energy and fixing carbon dioxide to produce organic molecules. A conserved and efficient network of light-dependent regulatory modules could be at the bases of this success. This regulatory system conferred early advantages to phototrophic eukaryotes that allowed for specialization, complex developmental processes and modern plant characteristics. We have studied light-dependent gene regulatory modules from algae to plants employing integrative-omics approaches based on gene co-expression networks. Our study reveals some remarkably conserved ways in which eukaryotic phototrophs deal with day length and light signaling. Here we describe how a family of Arabidopsis transcription factors involved in photoperiod response has evolved from a single algal gene according to the innovation, amplification and divergence theory of gene evolution by duplication. These modifications of the gene co-expression networks from the ancient unicellular green algae Chlamydomonas reinhardtii to the modern brassica Arabidopsis thaliana may hint on the evolution and specialization of plants and other organisms.

Mutation breeding of oil seed crops. Proceedings of a final research co-ordination meeting of an FAO/IAEA co-ordinated research programme held in Vienna, 11-15 January 1993

International Nuclear Information System (INIS)

1994-12-01

The document contains 19 papers presented at the final Research Co-ordination Meeting on 'Mutation Breeding of Oil Seed Crops' held in Vienna between 11-15 January 1993. A separate abstract was prepared for each paper. Refs, figs and tabs

A comprehensive analysis on preservation patterns of gene co-expression networks during Alzheimer's disease progression.

Science.gov (United States)

Ray, Sumanta; Hossain, Sk Md Mosaddek; Khatun, Lutfunnesa; Mukhopadhyay, Anirban

2017-12-20

Alzheimer's disease (AD) is a chronic neuro-degenerative disruption of the brain which involves in large scale transcriptomic variation. The disease does not impact every regions of the brain at the same time, instead it progresses slowly involving somewhat sequential interaction with different regions. Analysis of the expression patterns of the genes in different regions of the brain influenced in AD surely contribute for a enhanced comprehension of AD pathogenesis and shed light on the early characterization of the disease. Here, we have proposed a framework to identify perturbation and preservation characteristics of gene expression patterns across six distinct regions of the brain ("EC", "HIP", "PC", "MTG", "SFG", and "VCX") affected in AD. Co-expression modules were discovered considering a couple of regions at once. These are then analyzed to know the preservation and perturbation characteristics. Different module preservation statistics and a rank aggregation mechanism have been adopted to detect the changes of expression patterns across brain regions. Gene ontology (GO) and pathway based analysis were also carried out to know the biological meaning of preserved and perturbed modules. In this article, we have extensively studied the preservation patterns of co-expressed modules in six distinct brain regions affected in AD. Some modules are emerged as the most preserved while some others are detected as perturbed between a pair of brain regions. Further investigation on the topological properties of preserved and non-preserved modules reveals a substantial association amongst "betweenness centrality" and "degree" of the involved genes. Our findings may render a deeper realization of the preservation characteristics of gene expression patterns in discrete brain regions affected by AD.

Comparison of the precision of two standardized co-ordinate systems for the quantitation of brain anatomy: preliminary results.

Science.gov (United States)

Sandor, T; Tieman, J; Ong, H T; Moss, M B; Jolesz, F; Albert, M

1994-10-01

We assessed reproducible definition of two standardized co-ordinate systems for intersubject analysis of brain images. The baselines in the two co-ordinate systems were a modification of the canthomeatal (mCM) line and the anterior-posterior commissural (AC-PC) line. Axial spin-echo MR images of four subjects at 1.5T were used. Operator error was computed from the replicate analyses of two operators. The mCM line was determined by the lens of the eye and the internal auditory canal, and the AC-PC line was determined by the intersection of AC and PC with the interhemispheric fissure. Reproducibility of the mCM markers (SD = 0.59 mm) did not differ significantly from that of the AC-PC line (SD = 0.68 mm). The measurement error of the angle of the baseline (delta alpha), however, was more than 7 times as large for the AC-PC line as for the mCM line. An additional error affecting the rostrocaudal rotation of the co-ordinate systems, attributable to the distance between the anatomic markers, was 2.1 and 3.6 degrees (3 mm and 5 mm slice thickness) for the mCM co-ordinate system and 8.2 and 11.0 degrees (3 mm and 5 mm slice thickness) for the AC-PC system. The AC-PC line based co-ordinate system is therefore, less reproducible than the mCM line based system. This could be improved if a combination of axial and sagittal images were used for the definition of the AC-PC line.

Insulation co-ordination aspects for power stations with generator circuit-breakers

International Nuclear Information System (INIS)

Sanders, M.; Koeppl, G.; Kreuzer, J.

1995-01-01

The generator circuit-breaker (gen. c.b.) located between the generator and the step-up transformer, is now being applied world-wide. It has become a recognized electrical component of power stations which is largely due to economical advantages and increased power station availability. Technical protection considerations for power stations have always been the reason for discussion and the object of improvement. With the use of a gen. c.b., some points of view need to be considered anew. Not only the protection system in case of fault conditions will be influenced, but also the insulation co-ordination philosophy. Below the results of some calculations concerning expected overvoltages are presented. These calculations are based on a transformer rated 264/15.5kV, 220 MVA. But the results are transferable to other power plants. Some measurements carried out on a transformer of the same rating complement the calculations. The findings may contribute to an improvement in insulation co-ordination and protection of the electrical system generator--step-up transformer

Nuclear based technologies for estimating microbial protein supply in ruminant livestock. Proceedings of the second research co-ordination meeting of a co-ordinated research project (phase 1)

International Nuclear Information System (INIS)

1999-06-01

The Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture through its Co-ordinated Research Projects (CRPs), has been assisting national agricultural research systems in Member States to develop and apply nuclear and related techniques for improving livestock productivity. The programmes have focused on animal nutrition, animal reproduction and more recently on animal nutrition/reproduction interactions with emphasis on smallholder farming systems. The measurement of microbial protein supply to ruminant livestock has been an important area of research in ruminant nutrition. An estimate of microbial protein contribution to the intestinal protein flow is important for estimating the protein requirement of ruminant animals. Understanding the process of microbial protein synthesis has been difficult however, and due to the lack of simple and accurate methods for measuring microbial protein production in vivo, the methods used are based on complex microbial markers which require surgically prepared animals. As a result of a consultants meeting held in May 1995 to advise the Joint FAO/IAEA Division on the feasibility of using nuclear and related techniques for the development and validation of techniques for measuring microbial protein supply in ruminant animals, an FAO/IAEA Co-ordinated Research Project on Development, Standardization and Validation of Nuclear Based Technologies for Measuring Microbial Protein Supply in Ruminant Livestock for Improving Productivity was initiated in 1996, with a view to validating and adapting this technology for use in developing countries. To assist scientists participating in the CRP, a laboratory manual containing experimental protocols and methodologies for standardization and validation of the urine purine derivative technique and the development of models to suit local conditions, was published as IAEA-TECDOC-945. The present publication contains the final reports from participants in Phase 1 of the project

Nuclear based technologies for estimating microbial protein supply in ruminant livestock. Proceedings of the second research co-ordination meeting of a co-ordinated research project (phase 1)

Energy Technology Data Exchange (ETDEWEB)

NONE

1999-06-01

The Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture through its Co-ordinated Research Projects (CRPs), has been assisting national agricultural research systems in Member States to develop and apply nuclear and related techniques for improving livestock productivity. The programmes have focused on animal nutrition, animal reproduction and more recently on animal nutrition/reproduction interactions with emphasis on smallholder farming systems. The measurement of microbial protein supply to ruminant livestock has been an important area of research in ruminant nutrition. An estimate of microbial protein contribution to the intestinal protein flow is important for estimating the protein requirement of ruminant animals. Understanding the process of microbial protein synthesis has been difficult however, and due to the lack of simple and accurate methods for measuring microbial protein production in vivo, the methods used are based on complex microbial markers which require surgically prepared animals. As a result of a consultants meeting held in May 1995 to advise the Joint FAO/IAEA Division on the feasibility of using nuclear and related techniques for the development and validation of techniques for measuring microbial protein supply in ruminant animals, an FAO/IAEA Co-ordinated Research Project on Development, Standardization and Validation of Nuclear Based Technologies for Measuring Microbial Protein Supply in Ruminant Livestock for Improving Productivity was initiated in 1996, with a view to validating and adapting this technology for use in developing countries. To assist scientists participating in the CRP, a laboratory manual containing experimental protocols and methodologies for standardization and validation of the urine purine derivative technique and the development of models to suit local conditions, was published as IAEA-TECDOC-945. The present publication contains the final reports from participants in Phase 1 of the project

A Coding of Real Null Four-Momenta into World-Sheet Co-ordinates

OpenAIRE

Fairlie, David B.

2008-01-01

The results of minimizing the action for string-like systems on a simply-connected world sheet are shown to encode the Cartesian components of real null momentum four-vectors into co-ordinates on the world sheet. This identification arises consistently from different approaches to the problem.

Genetic architecture of gene expression in the chicken

Directory of Open Access Journals (Sweden)

Stanley Dragana

2013-01-01

Full Text Available Abstract Background The annotation of many genomes is limited, with a large proportion of identified genes lacking functional assignments. The construction of gene co-expression networks is a powerful approach that presents a way of integrating information from diverse gene expression datasets into a unified analysis which allows inferences to be drawn about the role of previously uncharacterised genes. Using this approach, we generated a condition-free gene co-expression network for the chicken using data from 1,043 publically available Affymetrix GeneChip Chicken Genome Arrays. This data was generated from a diverse range of experiments, including different tissues and experimental conditions. Our aim was to identify gene co-expression modules and generate a tool to facilitate exploration of the functional chicken genome. Results Fifteen modules, containing between 24 and 473 genes, were identified in the condition-free network. Most of the modules showed strong functional enrichment for particular Gene Ontology categories. However, a few showed no enrichment. Transcription factor binding site enrichment was also noted. Conclusions We have demonstrated that this chicken gene co-expression network is a useful tool in gene function prediction and the identification of putative novel transcription factors and binding sites. This work highlights the relevance of this methodology for functional prediction in poorly annotated genomes such as the chicken.

Seven-co-ordination in chlorohexakis(trimethylphosphine oxide)- uranium(IV) trichloride: crystal and molecular structure

Energy Technology Data Exchange (ETDEWEB)

Bombieri, G; Forsellini, E [Consiglio Nazionale delle Ricerche, Padua (Italy). Lab. di Chimica e Tecnologia dei Radioelementi; Brown, D; Whittaker, B

1976-01-01

The structure of the title compound has been determined by single-crystal X-ray diffraction methods from diffractometer data and refined to a final R of 0.023. The compound crystallises in space group R3c with asub(hex) = 18.447(3), csub(hex) = 19.348(3) A, Z = 6. The uranium atom is co-ordinated to one chlorine (U-Cl 2.813 A) and six oxygen atoms (mean U-O 2.26 A); the co-ordination polyhedron can be described as a distorted monocapped trigonal antiprism or as a distorted monocapped octahedron. The anionic chlorines are more than 6.22 A from the uranium atoms. The results are discussed in relation to spectral data for this and related uranium(IV) complexes.

Seven-co-ordination in chlorohexakis(trimethylphosphine oxide)- uranium(IV) trichloride: crystal and molecular structure

International Nuclear Information System (INIS)

Bombieri, G.; Forsellini, E.; Brown, D.; Whittaker, B.

1976-01-01

The structure of the title compound has been determined by single-crystal X-ray diffraction methods from diffractometer data and refined to a final R of 0.023. The compound crystallises in space group R3c with asub(hex) = 18.447(3), csub(hex) = 19.348(3) A, Z = 6. The uranium atom is co-ordinated to one chlorine (U-Cl 2.813 A) and six oxygen atoms (mean U-O 2.26 A); the co-ordination polyhedron can be described as a distorted monocapped trigonal antiprism or as a distorted monocapped octahedron. The anionic chlorines are more than 6.22 A from the uranium atoms. The results are discussed in relation to spectral data for this and related uranium(IV) complexes. (author)

Insulation co-ordination in high-voltage electric power systems

CERN Document Server

Diesendorf, W

2015-01-01

Insulation Co-ordination in High-Voltage Electric Power Systems deals with the methods of insulation needed in different circumstances. The book covers topics such as overvoltages and lightning surges; disruptive discharge and withstand voltages; self-restoring and non-self-restoring insulation; lightning overvoltages on transmission lines; and the attenuation and distortion of lightning surges. Also covered in the book are topics such as the switching surge designs of transmission lines, as well as the insulation coordination of high-voltage stations. The text is recommended for electrical en

Co-ordinated research project on application of nuclear techniques in the prevention of degenerative diseases (obesity and non-Insulin dependent diseases) in ageing. Report on the second research co-ordination meeting

Energy Technology Data Exchange (ETDEWEB)

NONE

2002-07-01

In the developed countries, research using nuclear methods has been substantially used to examine the physiological and biochemical mechanisms involved in obesity-related diseases. This Co-ordinated Research Project (CRP) is intended to promote the use of these techniques in the developing world. The specific objectives of this CRP are: 1. To define the magnitude of the obesity/NIDDM problem in developing countries. 2. To identify vulnerable groups at high risk. 3. To describe the metabolic mechanisms involved. The purpose of this first Research Co-ordination Meeting (RCM) was thus to develop a worldwide collaboration in the use of nuclear and isotopic techniques to investigate the aetiology of degenerative diseases in ageing. All countries participating in this CRP are going through the epidemiological transition with changes in lifestyles to approach those seen in the developed nations.

Co-ordinated research project on application of nuclear techniques in the prevention of degenerative diseases (obesity and non-Insulin dependent diseases) in ageing. Report on the second research co-ordination meeting

International Nuclear Information System (INIS)

2002-01-01

In the developed countries, research using nuclear methods has been substantially used to examine the physiological and biochemical mechanisms involved in obesity-related diseases. This Co-ordinated Research Project (CRP) is intended to promote the use of these techniques in the developing world. The specific objectives of this CRP are: 1. To define the magnitude of the obesity/NIDDM problem in developing countries. 2. To identify vulnerable groups at high risk. 3. To describe the metabolic mechanisms involved. The purpose of this first Research Co-ordination Meeting (RCM) was thus to develop a worldwide collaboration in the use of nuclear and isotopic techniques to investigate the aetiology of degenerative diseases in ageing. All countries participating in this CRP are going through the epidemiological transition with changes in lifestyles to approach those seen in the developed nations

Co-ordination properties of diglycol-amide (DGA) to trivalent curium and lanthanides studied by XAS, XRD and XPS methods

International Nuclear Information System (INIS)

Yaita, T.; Hirata, M.; Narita, H.; Tachimori, S.; Yamamoto, H.; Edelstein, N.M.; Bucher, J.J.; Shuh, D.K.; Rao, L.

2001-01-01

Co-ordination properties of diglycol-amide (DGA) to trivalent curium and to the trivalent lanthanides were studied by the EXAFS, the XRD and the XPS methods. The structural determinations by both the crystal XRD and the solution EXAFS methods showed that the DGA co-ordinated to the trivalent lanthanide ion in a tridentate fashion: co-ordination of three oxygen atoms of each ligand to the metal ion. The bond distances of Er-O (carbonyl) and Er-O (ether) in the Er-DGA complex were 2.35 Angstrom, and 2.46 Angstrom, respectively, while the atom distances of Cm-O (carbonyl) and Cm-O (ether) in the Cm-DGA complex were 2.42 Angstrom and 3.94 Angstrom, respectively from the EXAFS data for the Cm-DGA complex. Accordingly, the DGA would behave only as a semi-tridentate in the co-ordination to trivalent curium in solution. We determined the valence band structures of the Er-DGA complex by the XPS in order to clarify the bond properties of the complex, and assigned the XPS spectrum by using the DV-DS molecular orbital calculation method. (authors)

[Weighted gene co-expression network analysis in biomedicine research].

Science.gov (United States)

Liu, Wei; Li, Li; Ye, Hua; Tu, Wei

2017-11-25

High-throughput biological technologies are now widely applied in biology and medicine, allowing scientists to monitor thousands of parameters simultaneously in a specific sample. However, it is still an enormous challenge to mine useful information from high-throughput data. The emergence of network biology provides deeper insights into complex bio-system and reveals the modularity in tissue/cellular networks. Correlation networks are increasingly used in bioinformatics applications. Weighted gene co-expression network analysis (WGCNA) tool can detect clusters of highly correlated genes. Therefore, we systematically reviewed the application of WGCNA in the study of disease diagnosis, pathogenesis and other related fields. First, we introduced principle, workflow, advantages and disadvantages of WGCNA. Second, we presented the application of WGCNA in disease, physiology, drug, evolution and genome annotation. Then, we indicated the application of WGCNA in newly developed high-throughput methods. We hope this review will help to promote the application of WGCNA in biomedicine research.

Gene co-expression networks and profiles reveal potential biomarkers of boar taint in pigs

DEFF Research Database (Denmark)

Drag, Markus; Skinkyté-Juskiené, R.; Do, Duy Ngoc

synthesis. In testis, >80 DE genes were functionally classified by the PANTHER tool to “Gonadotropin releasing hormone receptor” and “Wnt signaling” pathways which play a role in reproductive maturation and proliferation of spermatogonia, respectively. WGCNA was used to build co-expression modules...

Developing a Patient Care Co-ordination Centre in Trafford, England: lessons from the International Foundation for Integrated Care (IFIC/Advancing Quality Alliance integrated care fellowship experience

Directory of Open Access Journals (Sweden)

Michael Gregory

2015-05-01

Full Text Available The NHS and Social Care in England are facing one of the biggest financial challenges for a generation. Commissioners and providers need to work on collaborative schemes to manage the increasing demand on health and social care within a period of financial constraint. Different forms of care co-ordination have been developed at different levels across the world.In the north-west of England, the Trafford health and social care economy have been working through a competitive dialogue process with industry to develop an innovative and dynamic solution to deliver seamless co-ordination for all patients and service users. The strategy is to develop a new Patient Care Co-ordination Centre, which will be responsible for the delivery of co-ordinated, quality care. The Patient Care Co-ordination Centre will work at clinical, service, functional and community levels across multiple providers covering risk stratification, preventative, elective and unscheduled care.I am the clinical lead for the Patient Care Co-ordination Centre and during my year as an Advancing Quality Alliance Integrated Care Fellow, I have had the opportunity to study examples of care coordination from UK and international sites. The learning from these visits has been assimilated into the design process of the Patient Care Co-ordination Centre.

Developing a Patient Care Co-ordination Centre in Trafford, England: lessons from the International Foundation for Integrated Care (IFIC)/Advancing Quality Alliance integrated care fellowship experience.

Science.gov (United States)

Gregory, Michael

2015-01-01

The NHS and Social Care in England are facing one of the biggest financial challenges for a generation. Commissioners and providers need to work on collaborative schemes to manage the increasing demand on health and social care within a period of financial constraint. Different forms of care co-ordination have been developed at different levels across the world. In the north-west of England, the Trafford health and social care economy have been working through a competitive dialogue process with industry to develop an innovative and dynamic solution to deliver seamless co-ordination for all patients and service users. The strategy is to develop a new Patient Care Co-ordination Centre, which will be responsible for the delivery of co-ordinated, quality care. The Patient Care Co-ordination Centre will work at clinical, service, functional and community levels across multiple providers covering risk stratification, preventative, elective and unscheduled care. I am the clinical lead for the Patient Care Co-ordination Centre and during my year as an Advancing Quality Alliance Integrated Care Fellow, I have had the opportunity to study examples of care coordination from UK and international sites. The learning from these visits has been assimilated into the design process of the Patient Care Co-ordination Centre.

Developing a Patient Care Co-ordination Centre in Trafford, England: lessons from the International Foundation for Integrated Care (IFIC/Advancing Quality Alliance integrated care fellowship experience

Directory of Open Access Journals (Sweden)

Michael Gregory

2015-05-01

Full Text Available The NHS and Social Care in England are facing one of the biggest financial challenges for a generation. Commissioners and providers need to work on collaborative schemes to manage the increasing demand on health and social care within a period of financial constraint. Different forms of care co-ordination have been developed at different levels across the world. In the north-west of England, the Trafford health and social care economy have been working through a competitive dialogue process with industry to develop an innovative and dynamic solution to deliver seamless co-ordination for all patients and service users. The strategy is to develop a new Patient Care Co-ordination Centre, which will be responsible for the delivery of co-ordinated, quality care. The Patient Care Co-ordination Centre will work at clinical, service, functional and community levels across multiple providers covering risk stratification, preventative, elective and unscheduled care. I am the clinical lead for the Patient Care Co-ordination Centre and during my year as an Advancing Quality Alliance Integrated Care Fellow, I have had the opportunity to study examples of care coordination from UK and international sites. The learning from these visits has been assimilated into the design process of the Patient Care Co-ordination Centre.

Copying you copying me: interpersonal motor co-ordination influences automatic imitation.

Directory of Open Access Journals (Sweden)

Daniel Joel Shaw

Full Text Available Moving in a co-ordinated fashion with another individual changes our behaviour towards them; we tend to like them more, find them more attractive, and are more willing to co-operate with them. It is generally assumed that this effect on behaviour results from alterations in representations of self and others. Specifically, through neurophysiological perception-action matching mechanisms, interpersonal motor co-ordination (IMC is believed to forge a neural coupling between actor and observer, which serves to blur boundaries in conceptual self-other representations and causes positive views of the self to be projected onto others. An investigation into this potential neural mechanism is lacking, however. Moreover, the specific components of IMC that might influence this mechanism have not yet been specified. In the present study we exploited a robust behavioural phenomenon--automatic imitation--to assess the degree to which IMC influences neural action observation-execution matching mechanisms. This revealed that automatic imitation is reduced when the actions of another individual are perceived to be synchronised in time, but are spatially incongruent, with our own. We interpret our findings as evidence that IMC does indeed exert an effect on neural perception-action matching mechanisms, but this serves to promote better self-other distinction. Our findings demonstrate that further investigation is required to understand the complex relationship between neural perception-action coupling, conceptual self-other representations, and social behaviour.

Cogena, a novel tool for co-expressed gene-set enrichment analysis, applied to drug repositioning and drug mode of action discovery.

Science.gov (United States)

Jia, Zhilong; Liu, Ying; Guan, Naiyang; Bo, Xiaochen; Luo, Zhigang; Barnes, Michael R

2016-05-27

Drug repositioning, finding new indications for existing drugs, has gained much recent attention as a potentially efficient and economical strategy for accelerating new therapies into the clinic. Although improvement in the sensitivity of computational drug repositioning methods has identified numerous credible repositioning opportunities, few have been progressed. Arguably the "black box" nature of drug action in a new indication is one of the main blocks to progression, highlighting the need for methods that inform on the broader target mechanism in the disease context. We demonstrate that the analysis of co-expressed genes may be a critical first step towards illumination of both disease pathology and mode of drug action. We achieve this using a novel framework, co-expressed gene-set enrichment analysis (cogena) for co-expression analysis of gene expression signatures and gene set enrichment analysis of co-expressed genes. The cogena framework enables simultaneous, pathway driven, disease and drug repositioning analysis. Cogena can be used to illuminate coordinated changes within disease transcriptomes and identify drugs acting mechanistically within this framework. We illustrate this using a psoriatic skin transcriptome, as an exemplar, and recover two widely used Psoriasis drugs (Methotrexate and Ciclosporin) with distinct modes of action. Cogena out-performs the results of Connectivity Map and NFFinder webservers in similar disease transcriptome analyses. Furthermore, we investigated the literature support for the other top-ranked compounds to treat psoriasis and showed how the outputs of cogena analysis can contribute new insight to support the progression of drugs into the clinic. We have made cogena freely available within Bioconductor or https://github.com/zhilongjia/cogena . In conclusion, by targeting co-expressed genes within disease transcriptomes, cogena offers novel biological insight, which can be effectively harnessed for drug discovery and

Biotin augments acetyl CoA carboxylase 2 gene expression in the hypothalamus, leading to the suppression of food intake in mice.

Science.gov (United States)

Sone, Hideyuki; Kamiyama, Shin; Higuchi, Mutsumi; Fujino, Kaho; Kubo, Shizuka; Miyazawa, Masami; Shirato, Saya; Hiroi, Yuka; Shiozawa, Kota

2016-07-29

It is known that biotin prevents the development of diabetes by increasing the functions of pancreatic beta-cells and improving insulin sensitivity in the periphery. However, its anti-obesity effects such as anorectic effects remain to be clarified. Acetyl CoA carboxylase (ACC), a biotin-dependent enzyme, has two isoforms (ACC1 and ACC2) and serves to catalyze the reaction of acetyl CoA to malonyl CoA. In the hypothalamus, ACC2 increases the production of malonyl CoA, which acts as a satiety signal. In this study, we investigated whether biotin increases the gene expression of ACC2 in the hypothalamus and suppresses food intake in mice administered excessive biotin. Food intake was significantly decreased by biotin, but plasma regulators of appetite, including glucose, ghrelin, and leptin, were not affected. On the other hand, biotin notably accumulated in the hypothalamus and enhanced ACC2 gene expression there, but it did not change the gene expression of ACC1, malonyl CoA decarboxylase (a malonyl CoA-degrading enzyme), and AMP-activated protein kinase α-2 (an ACC-inhibitory enzyme). These findings strongly suggest that biotin potentiates the suppression of appetite by upregulating ACC2 gene expression in the hypothalamus. This effect of biotin may contribute to the prevention of diabetes by biotin treatment. Copyright © 2016 Elsevier Inc. All rights reserved.

Polycistronic gene expression in Aspergillus niger.

Science.gov (United States)

Schuetze, Tabea; Meyer, Vera

2017-09-25

Genome mining approaches predict dozens of biosynthetic gene clusters in each of the filamentous fungal genomes sequenced so far. However, the majority of these gene clusters still remain cryptic because they are not expressed in their natural host. Simultaneous expression of all genes belonging to a biosynthetic pathway in a heterologous host is one approach to activate biosynthetic gene clusters and to screen the metabolites produced for bioactivities. Polycistronic expression of all pathway genes under control of a single and tunable promoter would be the method of choice, as this does not only simplify cloning procedures, but also offers control on timing and strength of expression. However, polycistronic gene expression is a feature not commonly found in eukaryotic host systems, such as Aspergillus niger. In this study, we tested the suitability of the viral P2A peptide for co-expression of three genes in A. niger. Two genes descend from Fusarium oxysporum and are essential to produce the secondary metabolite enniatin (esyn1, ekivR). The third gene (luc) encodes the reporter luciferase which was included to study position effects. Expression of the polycistronic gene cassette was put under control of the Tet-On system to ensure tunable gene expression in A. niger. In total, three polycistronic expression cassettes which differed in the position of luc were constructed and targeted to the pyrG locus in A. niger. This allowed direct comparison of the luciferase activity based on the position of the luciferase gene. Doxycycline-mediated induction of the Tet-On expression cassettes resulted in the production of one long polycistronic mRNA as proven by Northern analyses, and ensured comparable production of enniatin in all three strains. Notably, gene position within the polycistronic expression cassette matters, as, luciferase activity was lowest at position one and had a comparable activity at positions two and three. The P2A peptide can be used to express at

Domestication rewired gene expression and nucleotide diversity patterns in tomato.

Science.gov (United States)

Sauvage, Christopher; Rau, Andrea; Aichholz, Charlotte; Chadoeuf, Joël; Sarah, Gautier; Ruiz, Manuel; Santoni, Sylvain; Causse, Mathilde; David, Jacques; Glémin, Sylvain

2017-08-01

Plant domestication has led to considerable phenotypic modifications from wild species to modern varieties. However, although changes in key traits have been well documented, less is known about the underlying molecular mechanisms, such as the reduction of molecular diversity or global gene co-expression patterns. In this study, we used a combination of gene expression and population genetics in wild and crop tomato to decipher the footprints of domestication. We found a set of 1729 differentially expressed genes (DEG) between the two genetic groups, belonging to 17 clusters of co-expressed DEG, suggesting that domestication affected not only individual genes but also regulatory networks. Five co-expression clusters were enriched in functional terms involving carbohydrate metabolism or epigenetic regulation of gene expression. We detected differences in nucleotide diversity between the crop and wild groups specific to DEG. Our study provides an extensive profiling of the rewiring of gene co-expression induced by the domestication syndrome in one of the main crop species. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Dissection of regulatory networks that are altered in disease via differential co-expression.

Directory of Open Access Journals (Sweden)

David Amar

Full Text Available Comparing the gene-expression profiles of sick and healthy individuals can help in understanding disease. Such differential expression analysis is a well-established way to find gene sets whose expression is altered in the disease. Recent approaches to gene-expression analysis go a step further and seek differential co-expression patterns, wherein the level of co-expression of a set of genes differs markedly between disease and control samples. Such patterns can arise from a disease-related change in the regulatory mechanism governing that set of genes, and pinpoint dysfunctional regulatory networks. Here we present DICER, a new method for detecting differentially co-expressed gene sets using a novel probabilistic score for differential correlation. DICER goes beyond standard differential co-expression and detects pairs of modules showing differential co-expression. The expression profiles of genes within each module of the pair are correlated across all samples. The correlation between the two modules, however, differs markedly between the disease and normal samples. We show that DICER outperforms the state of the art in terms of significance and interpretability of the detected gene sets. Moreover, the gene sets discovered by DICER manifest regulation by disease-specific microRNA families. In a case study on Alzheimer's disease, DICER dissected biological processes and protein complexes into functional subunits that are differentially co-expressed, thereby revealing inner structures in disease regulatory networks.

The gene expression profiles of canine mammary cancer cells grown with carcinoma-associated fibroblasts (CAFs as a co-culture in vitro

Directory of Open Access Journals (Sweden)

Król Magdalena

2012-03-01

Full Text Available Abstract Background It is supposed that fibroblasts present in tumour microenvironment increase cancer invasiveness and its ability to metastasize but the mechanisms have not been clearly defined yet. Thus, the current study was designed to assess changes in gene expression in five various cancer cell lines grown as a co-culture with the carcinoma-associated fibroblasts (CAFs in vitro. Results A carcinoma-associated fibroblast cell line was isolated from a canine mammary cancer. Then, a co-culture of cancer cells with the CAFs was established and maintained for 72 hrs. Having sorted the cells, a global gene expression in cancer cells using DNA microarrays was examined. The analysis revealed an up-regulation of 100 genes and a down-regulation of 106 genes in the cancer cells grown as a co-culture with the CAFs in comparison to control conditions. The PANTHER binomial statistics tool was applied to determine statistically over-manifested pathways (p Conclusion The results of the current study showed that the co-culturing of cancer cells and the CAFs caused significant changes to the cancer gene expression. The presence of the CAFs in a microenvironment of cancer cells promotes adhesion, angiogenesis and EMT.

Nuclear Safety Co-Ordination within Oak Ridge Operations Facilities

Energy Technology Data Exchange (ETDEWEB)

Johnson, W. A.; Pryor, W. A. [Research and Development Division, United States Atomic Energy Commission, Oak Ridge, TN (United States)

1966-05-15

The Oak Ridge Operations Office of the USAEC has within its jurisdiction multiple contractors and facilities for research and for the production of fissile materials for the atomic energy programme. Among these facilities are gaseous diffusion plants for the production of {sup 235}U-enriched uranium hexafluoride, plants for the fabrication of special components and fuel for research and production reactors, and laboratories for pilot plant studies and basic research in nuclear technology. One research laboratory is also actively engaged in criticality experimental programmes and has been a major contributor of criticality data for safety applications. These diversified programmes include the processing, fabrication and transport of practically all forms and isotopic enrichments of uranium in quantities commensurate with both laboratory and volume production requirements. Consequently, adequate nuclear safety control with reasonable economy for operations of this magnitude demands not only co-ordination and liaison between contractor and USAEC staffs, but a continuing reappraisal of safety applications in light of the most advanced information. This report outlines the role of the Oak Ridge Operations Office in these pursuits and describes as examples some specific problems in which this office co-ordinated actions necessary for their resolution. Other examples are given of parametric and procedural applications in plant processes and fissile shipments emphasizing the use of recent experimental or calculated data. These examples involve the use of mass and geometric variables, neutron absorbers and moderation control. Departures from limits specified in existing nuclear safety guides are made to advantage in light of new data, special equipment design, contingencies and acceptable risks. (author)

Identification of a 251 gene expression signature that can accurately detect M. tuberculosis in patients with and without HIV co-infection.

Directory of Open Access Journals (Sweden)

Noor Dawany

Full Text Available BACKGROUND: Co-infection with tuberculosis (TB is the leading cause of death in HIV-infected individuals. However, diagnosis of TB, especially in the presence of an HIV co-infection, can be limiting due to the high inaccuracy associated with the use of conventional diagnostic methods. Here we report a gene signature that can identify a tuberculosis infection in patients co-infected with HIV as well as in the absence of HIV. METHODS: We analyzed global gene expression data from peripheral blood mononuclear cell (PBMC samples of patients that were either mono-infected with HIV or co-infected with HIV/TB and used support vector machines to identify a gene signature that can distinguish between the two classes. We then validated our results using publically available gene expression data from patients mono-infected with TB. RESULTS: Our analysis successfully identified a 251-gene signature that accurately distinguishes patients co-infected with HIV/TB from those infected with HIV only, with an overall accuracy of 81.4% (sensitivity = 76.2%, specificity = 86.4%. Furthermore, we show that our 251-gene signature can also accurately distinguish patients with active TB in the absence of an HIV infection from both patients with a latent TB infection and healthy controls (88.9-94.7% accuracy; 69.2-90% sensitivity and 90.3-100% specificity. We also demonstrate that the expression levels of the 251-gene signature diminish as a correlate of the length of TB treatment. CONCLUSIONS: A 251-gene signature is described to (a detect TB in the presence or absence of an HIV co-infection, and (b assess response to treatment following anti-TB therapy.

Weighted Gene Co-expression Network Analysis of the Dioscin Rich Medicinal Plant Dioscorea nipponica

Directory of Open Access Journals (Sweden)

Wei Sun

2017-06-01

Full Text Available Dioscorea contains critically important species which can be used as staple foods or sources of bioactive substances, including Dioscorea nipponica, which has been used to develop highly successful drugs to treat cardiovascular disease. Its major active ingredients are thought to be sterol compounds such as diosgenin, which has been called “medicinal gold” because of its valuable properties. However, reliance on naturally growing plants as a production system limits the potential use of D. nipponica, raising interest in engineering metabolic pathways to enhance the production of secondary metabolites. However, the biosynthetic pathway of diosgenin is still poorly understood, and D. nipponica is poorly characterized at a molecular level, hindering in-depth investigation. In the present work, the RNAs from five organs and seven methyl jasmonate treated D. nipponica rhizomes were sequenced using the Illumina high-throughput sequencing platform, yielding 52 gigabases of data, which were pooled and assembled into a reference transcriptome. Four hundred and eighty two genes were found to be highly expressed in the rhizomes, and these genes are mainly involved in stress response and transcriptional regulation. Based on their expression patterns, 36 genes were selected for further investigation as candidate genes involved in dioscin biosynthesis. Constructing co-expression networks based on significant changes in gene expression revealed 15 gene modules. Of these, four modules with properties correlating to dioscin regulation and biosynthesis, consisting of 4,665 genes in total, were selected for further functional investigation. These results improve our understanding of dioscin biosynthesis in this important medicinal plant and will help guide more intensive investigations.

Co-ordinated expression of MMP-2 and its putative activator, MT1-MMP, in human placentation.

Science.gov (United States)

Bjørn, S F; Hastrup, N; Lund, L R; Danø, K; Larsen, J F; Pyke, C

1997-08-01

The spatial expression of mRNA for matrix metalloproteinase 2 (MMP-2), its putative activator, the membrane-type 1 matrix metalloproteinase (MT1-MMP), and the MMP-2 substrate type IV collagen was investigated in human placentas of both normal and tubal ectopic pregnancies and in cyclic endometrium using in-situ hybridization. Cytokeratin staining applied to adjacent sections was used to identify epithelial and trophoblast cells. In both normal and tubal pregnancies MT1-MMP, MMP-2 and type IV collagen mRNA were highly expressed and co-localized in the extravillous cytotrophoblasts of anchoring villi, in cytotrophoblasts that had penatrated into the placental bed and in cytotrophoblastic cell islands. In addition, the decidual cells of normal pregnancies in some areas co-expressed MT1-MMP and MMP-2 mRNA, with moderate signals for both components. Fibroblast-like stromal cells in tubal pregnancies were positive for MMP-2 mRNA but generally negative for MT1-MMP mRNA. The consistent co-localization of MT1-MMP with MMP-2 and type IV collagen in the same subset of cytotrophoblasts strongly suggests that all three components co-operate in the tightly regulated fetal invasion process. The co-expression of MT1-MMP and MMP-2 mRNA in some of the decidual cells indicates that these cells are also actively involved in the placentation process.

Transitions from mono- to co- to tri-culture uniquely affect gene expression in breast cancer, stromal, and immune compartments.

Science.gov (United States)

Regier, Mary C; Maccoux, Lindsey J; Weinberger, Emma M; Regehr, Keil J; Berry, Scott M; Beebe, David J; Alarid, Elaine T

2016-08-01

Heterotypic interactions in cancer microenvironments play important roles in disease initiation, progression, and spread. Co-culture is the predominant approach used in dissecting paracrine interactions between tumor and stromal cells, but functional results from simple co-cultures frequently fail to correlate to in vivo conditions. Though complex heterotypic in vitro models have improved functional relevance, there is little systematic knowledge of how multi-culture parameters influence this recapitulation. We therefore have employed a more iterative approach to investigate the influence of increasing model complexity; increased heterotypic complexity specifically. Here we describe how the compartmentalized and microscale elements of our multi-culture device allowed us to obtain gene expression data from one cell type at a time in a heterotypic culture where cells communicated through paracrine interactions. With our device we generated a large dataset comprised of cell type specific gene-expression patterns for cultures of increasing complexity (three cell types in mono-, co-, or tri-culture) not readily accessible in other systems. Principal component analysis indicated that gene expression was changed in co-culture but was often more strongly altered in tri-culture as compared to mono-culture. Our analysis revealed that cell type identity and the complexity around it (mono-, co-, or tri-culture) influence gene regulation. We also observed evidence of complementary regulation between cell types in the same heterotypic culture. Here we demonstrate the utility of our platform in providing insight into how tumor and stromal cells respond to microenvironments of varying complexities highlighting the expanding importance of heterotypic cultures that go beyond conventional co-culture.

First research co-ordination meeting of the co-ordinated research programme on development of kits for radioimmunometric assays for tumour markers. Summary report

International Nuclear Information System (INIS)

1997-01-01

Cancer is one of the major reasons for mortality and a great deal of research goes on in many areas related to cancer all through the world. The concept of 'tumor markers' has greatly aided the management of cancer, especially for follow up of the treated patients. Immunoassays that are used for measurement of sub-picomolar quantities of biomolecules such as hormones have been developed for the measurement of tumor markers too and these are widely used for monitoring the patients. The current co-ordinated research program on 'Development of Immunometric Assays for the Tumor Makers: PSA, free PSA and TPS' was born out of the advise from a group of specialists from the field oncology and nuclear medicine who met to discuss initially (Advisory Group Meeting, Colombo, August 1996) to identify the most appropriate markers and later (Consultants' Meeting, Glasgow, 21-25 April 1997) to identify the details of the procedure to follow. The first Research Co-ordination Meeting of this group was held in Vienna from 9-12 December 1997 to review the plans of each participant and the steps to be taken to realize the goal of this CRP. The meeting was attended by participants from the ten laboratories. The meeting discussed all salient aspects of the IRMA development for PSA and TPS. The modalities of working out the plans were thoroughly considered and the key inputs for the program to take off were identified. In conclusion, all the nine contract holding participants would develop the IRMAs for PSA (free and total) and TPS (Uruguay)

Nuclear techniques for toxic elements in foodstuffs. Report on an IAEA co-ordinated research programme

International Nuclear Information System (INIS)

1994-01-01

The document includes 10 final reports on the IAEA Co-ordinated Research Programme on Nuclear Techniques for Toxic Elements in Foodstuffs. A separate abstract was prepared for each report. Refs, figs and tabs

Nuclear techniques for toxic elements in foodstuffs. Report on an IAEA co-ordinated research programme

Energy Technology Data Exchange (ETDEWEB)

NONE

1994-12-31

The document includes 10 final reports on the IAEA Co-ordinated Research Programme on Nuclear Techniques for Toxic Elements in Foodstuffs. A separate abstract was prepared for each report. Refs, figs and tabs.

Mining disease genes using integrated protein-protein interaction and gene-gene co-regulation information.

Science.gov (United States)

Li, Jin; Wang, Limei; Guo, Maozu; Zhang, Ruijie; Dai, Qiguo; Liu, Xiaoyan; Wang, Chunyu; Teng, Zhixia; Xuan, Ping; Zhang, Mingming

2015-01-01

In humans, despite the rapid increase in disease-associated gene discovery, a large proportion of disease-associated genes are still unknown. Many network-based approaches have been used to prioritize disease genes. Many networks, such as the protein-protein interaction (PPI), KEGG, and gene co-expression networks, have been used. Expression quantitative trait loci (eQTLs) have been successfully applied for the determination of genes associated with several diseases. In this study, we constructed an eQTL-based gene-gene co-regulation network (GGCRN) and used it to mine for disease genes. We adopted the random walk with restart (RWR) algorithm to mine for genes associated with Alzheimer disease. Compared to the Human Protein Reference Database (HPRD) PPI network alone, the integrated HPRD PPI and GGCRN networks provided faster convergence and revealed new disease-related genes. Therefore, using the RWR algorithm for integrated PPI and GGCRN is an effective method for disease-associated gene mining.

Co-ordinated functions of Mms proteins define the surface structure of cubo-octahedral magnetite crystals in magnetotactic bacteria.

Science.gov (United States)

Arakaki, Atsushi; Yamagishi, Ayana; Fukuyo, Ayumi; Tanaka, Masayoshi; Matsunaga, Tadashi

2014-08-01

Magnetotactic bacteria synthesize magnetosomes comprised of membrane-enveloped single crystalline magnetite (Fe3 O4 ). The size and morphology of the nano-sized magnetite crystals (Mms (Mms5, Mms6, Mms7, and Mms13), was previously isolated from the surface of cubo-octahedral magnetite crystals in Magnetospirillum magneticum strain AMB-1. Analysis of an mms6 gene deletion mutant suggested that the Mms6 protein plays a major role in the regulation of magnetite crystal size and morphology. In this study, we constructed various mms gene deletion mutants and characterized the magnetite crystals formed by the mutant strains. Comparative analysis showed that all mms genes were involved in the promotion of crystal growth in different manners. The phenotypic characterization of magnetites also suggested that these proteins are involved in controlling the geometries of the crystal surface structures. Thus, the co-ordinated functions of Mms proteins regulate the morphology of the cubo-octahedral magnetite crystals in magnetotactic bacteria. © 2014 John Wiley & Sons Ltd.

ConGEMs: Condensed Gene Co-Expression Module Discovery Through Rule-Based Clustering and Its Application to Carcinogenesis

Directory of Open Access Journals (Sweden)

Saurav Mallik

2017-12-01

Full Text Available For transcriptomic analysis, there are numerous microarray-based genomic data, especially those generated for cancer research. The typical analysis measures the difference between a cancer sample-group and a matched control group for each transcript or gene. Association rule mining is used to discover interesting item sets through rule-based methodology. Thus, it has advantages to find causal effect relationships between the transcripts. In this work, we introduce two new rule-based similarity measures—weighted rank-based Jaccard and Cosine measures—and then propose a novel computational framework to detect condensed gene co-expression modules ( C o n G E M s through the association rule-based learning system and the weighted similarity scores. In practice, the list of evolved condensed markers that consists of both singular and complex markers in nature depends on the corresponding condensed gene sets in either antecedent or consequent of the rules of the resultant modules. In our evaluation, these markers could be supported by literature evidence, KEGG (Kyoto Encyclopedia of Genes and Genomes pathway and Gene Ontology annotations. Specifically, we preliminarily identified differentially expressed genes using an empirical Bayes test. A recently developed algorithm—RANWAR—was then utilized to determine the association rules from these genes. Based on that, we computed the integrated similarity scores of these rule-based similarity measures between each rule-pair, and the resultant scores were used for clustering to identify the co-expressed rule-modules. We applied our method to a gene expression dataset for lung squamous cell carcinoma and a genome methylation dataset for uterine cervical carcinogenesis. Our proposed module discovery method produced better results than the traditional gene-module discovery measures. In summary, our proposed rule-based method is useful for exploring biomarker modules from transcriptomic data.

ConGEMs: Condensed Gene Co-Expression Module Discovery Through Rule-Based Clustering and Its Application to Carcinogenesis.

Science.gov (United States)

Mallik, Saurav; Zhao, Zhongming

2017-12-28

For transcriptomic analysis, there are numerous microarray-based genomic data, especially those generated for cancer research. The typical analysis measures the difference between a cancer sample-group and a matched control group for each transcript or gene. Association rule mining is used to discover interesting item sets through rule-based methodology. Thus, it has advantages to find causal effect relationships between the transcripts. In this work, we introduce two new rule-based similarity measures-weighted rank-based Jaccard and Cosine measures-and then propose a novel computational framework to detect condensed gene co-expression modules ( C o n G E M s) through the association rule-based learning system and the weighted similarity scores. In practice, the list of evolved condensed markers that consists of both singular and complex markers in nature depends on the corresponding condensed gene sets in either antecedent or consequent of the rules of the resultant modules. In our evaluation, these markers could be supported by literature evidence, KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway and Gene Ontology annotations. Specifically, we preliminarily identified differentially expressed genes using an empirical Bayes test. A recently developed algorithm-RANWAR-was then utilized to determine the association rules from these genes. Based on that, we computed the integrated similarity scores of these rule-based similarity measures between each rule-pair, and the resultant scores were used for clustering to identify the co-expressed rule-modules. We applied our method to a gene expression dataset for lung squamous cell carcinoma and a genome methylation dataset for uterine cervical carcinogenesis. Our proposed module discovery method produced better results than the traditional gene-module discovery measures. In summary, our proposed rule-based method is useful for exploring biomarker modules from transcriptomic data.

Differential gene expression in human fibroblasts after alpha-particle emitter (211)At compared with (60)Co irradiation

DEFF Research Database (Denmark)

Danielsson, Anna; Claesson, Kristina; Parris, Toshima Z

2013-01-01

trastuzumab monoclonal antibody (0.25, 0.5, and 1 Gy) and (60)Co (1, 2, and 3 Gy). Results: We report gene expression profiles that distinguish the effect different radiation qualities and absorbed doses have on cellular functions in human fibroblasts. In addition, we identified commonly expressed transcripts...

Nuclear techniques to assess irrigation schedules for field crops. Results of a co-ordinated research programme

Energy Technology Data Exchange (ETDEWEB)

NONE

1996-06-01

This TECDOC summarizes the results of a Co-ordinated Research Programme on The Use of Nuclear and Related Techniques in Assessment of Irrigation Schedules of Field Crops to Increase Effective Use of Water in Irrigation Projects. The programme was carried out between 1990 and 1995 through the technical co-ordination of the Soil Fertility, Irrigation and Crop Production Section of the Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture of the International Atomic Energy Agency. Fourteen Member States of the IAEA and FAO carried out a series of field experiments aimed at improving irrigation water use efficiency through a type of irrigation scheduling known as deficit irrigation. Refs, figs, tabs.

Nuclear techniques to assess irrigation schedules for field crops. Results of a co-ordinated research programme

International Nuclear Information System (INIS)

1996-06-01

This TECDOC summarizes the results of a Co-ordinated Research Programme on The Use of Nuclear and Related Techniques in Assessment of Irrigation Schedules of Field Crops to Increase Effective Use of Water in Irrigation Projects. The programme was carried out between 1990 and 1995 through the technical co-ordination of the Soil Fertility, Irrigation and Crop Production Section of the Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture of the International Atomic Energy Agency. Fourteen Member States of the IAEA and FAO carried out a series of field experiments aimed at improving irrigation water use efficiency through a type of irrigation scheduling known as deficit irrigation. Refs, figs, tabs

Hi-C Chromatin Interaction Networks Predict Co-expression in the Mouse Cortex

Science.gov (United States)

Hulsman, Marc; Lelieveldt, Boudewijn P. F.; de Ridder, Jeroen; Reinders, Marcel

2015-01-01

The three dimensional conformation of the genome in the cell nucleus influences important biological processes such as gene expression regulation. Recent studies have shown a strong correlation between chromatin interactions and gene co-expression. However, predicting gene co-expression from frequent long-range chromatin interactions remains challenging. We address this by characterizing the topology of the cortical chromatin interaction network using scale-aware topological measures. We demonstrate that based on these characterizations it is possible to accurately predict spatial co-expression between genes in the mouse cortex. Consistent with previous findings, we find that the chromatin interaction profile of a gene-pair is a good predictor of their spatial co-expression. However, the accuracy of the prediction can be substantially improved when chromatin interactions are described using scale-aware topological measures of the multi-resolution chromatin interaction network. We conclude that, for co-expression prediction, it is necessary to take into account different levels of chromatin interactions ranging from direct interaction between genes (i.e. small-scale) to chromatin compartment interactions (i.e. large-scale). PMID:25965262

MPIGeneNet: Parallel Calculation of Gene Co-Expression Networks on Multicore Clusters.

Science.gov (United States)

Gonzalez-Dominguez, Jorge; Martin, Maria J

2017-10-10

In this work we present MPIGeneNet, a parallel tool that applies Pearson's correlation and Random Matrix Theory to construct gene co-expression networks. It is based on the state-of-the-art sequential tool RMTGeneNet, which provides networks with high robustness and sensitivity at the expenses of relatively long runtimes for large scale input datasets. MPIGeneNet returns the same results as RMTGeneNet but improves the memory management, reduces the I/O cost, and accelerates the two most computationally demanding steps of co-expression network construction by exploiting the compute capabilities of common multicore CPU clusters. Our performance evaluation on two different systems using three typical input datasets shows that MPIGeneNet is significantly faster than RMTGeneNet. As an example, our tool is up to 175.41 times faster on a cluster with eight nodes, each one containing two 12-core Intel Haswell processors. Source code of MPIGeneNet, as well as a reference manual, are available at https://sourceforge.net/projects/mpigenenet/.

Integrating Genetic and Gene Co-expression Analysis Identifies Gene Networks Involved in Alcohol and Stress Responses.

Science.gov (United States)

Luo, Jie; Xu, Pei; Cao, Peijian; Wan, Hongjian; Lv, Xiaonan; Xu, Shengchun; Wang, Gangjun; Cook, Melloni N; Jones, Byron C; Lu, Lu; Wang, Xusheng

2018-01-01

Although the link between stress and alcohol is well recognized, the underlying mechanisms of how they interplay at the molecular level remain unclear. The purpose of this study is to identify molecular networks underlying the effects of alcohol and stress responses, as well as their interaction on anxiety behaviors in the hippocampus of mice using a systems genetics approach. Here, we applied a gene co-expression network approach to transcriptomes of 41 BXD mouse strains under four conditions: stress, alcohol, stress-induced alcohol and control. The co-expression analysis identified 14 modules and characterized four expression patterns across the four conditions. The four expression patterns include up-regulation in no restraint stress and given an ethanol injection (NOE) but restoration in restraint stress followed by an ethanol injection (RSE; pattern 1), down-regulation in NOE but rescue in RSE (pattern 2), up-regulation in both restraint stress followed by a saline injection (RSS) and NOE, and further amplification in RSE (pattern 3), and up-regulation in RSS but reduction in both NOE and RSE (pattern 4). We further identified four functional subnetworks by superimposing protein-protein interactions (PPIs) to the 14 co-expression modules, including γ-aminobutyric acid receptor (GABA) signaling, glutamate signaling, neuropeptide signaling, cAMP-dependent signaling. We further performed module specificity analysis to identify modules that are specific to stress, alcohol, or stress-induced alcohol responses. Finally, we conducted causality analysis to link genetic variation to these identified modules, and anxiety behaviors after stress and alcohol treatments. This study underscores the importance of integrative analysis and offers new insights into the molecular networks underlying stress and alcohol responses.

Integrating Genetic and Gene Co-expression Analysis Identifies Gene Networks Involved in Alcohol and Stress Responses

Directory of Open Access Journals (Sweden)

Jie Luo

2018-04-01

Full Text Available Although the link between stress and alcohol is well recognized, the underlying mechanisms of how they interplay at the molecular level remain unclear. The purpose of this study is to identify molecular networks underlying the effects of alcohol and stress responses, as well as their interaction on anxiety behaviors in the hippocampus of mice using a systems genetics approach. Here, we applied a gene co-expression network approach to transcriptomes of 41 BXD mouse strains under four conditions: stress, alcohol, stress-induced alcohol and control. The co-expression analysis identified 14 modules and characterized four expression patterns across the four conditions. The four expression patterns include up-regulation in no restraint stress and given an ethanol injection (NOE but restoration in restraint stress followed by an ethanol injection (RSE; pattern 1, down-regulation in NOE but rescue in RSE (pattern 2, up-regulation in both restraint stress followed by a saline injection (RSS and NOE, and further amplification in RSE (pattern 3, and up-regulation in RSS but reduction in both NOE and RSE (pattern 4. We further identified four functional subnetworks by superimposing protein-protein interactions (PPIs to the 14 co-expression modules, including γ-aminobutyric acid receptor (GABA signaling, glutamate signaling, neuropeptide signaling, cAMP-dependent signaling. We further performed module specificity analysis to identify modules that are specific to stress, alcohol, or stress-induced alcohol responses. Finally, we conducted causality analysis to link genetic variation to these identified modules, and anxiety behaviors after stress and alcohol treatments. This study underscores the importance of integrative analysis and offers new insights into the molecular networks underlying stress and alcohol responses.

Co-ordinate regulation of cytokinin gene family members during flag leaf and reproductive development in wheat.

Science.gov (United States)

Song, Jiancheng; Jiang, Lijun; Jameson, Paula Elizabeth

2012-06-06

As the global population continues to expand, increasing yield in bread wheat is of critical importance as 20% of the world's food supply is sourced from this cereal. Several recent studies of the molecular basis of grain yield indicate that the cytokinins are a key factor in determining grain yield. In this study, cytokinin gene family members in bread wheat were isolated from four multigene families which regulate cytokinin synthesis and metabolism, the isopentenyl transferases (IPT), cytokinin oxidases (CKX), zeatin O-glucosyltransferases (ZOG), and β-glucosidases (GLU). As bread wheat is hexaploid, each gene family is also likely to be represented on the A, B and D genomes. By using a novel strategy of qRT-PCR with locus-specific primers shared among the three homoeologues of each family member, detailed expression profiles are provided of family members of these multigene families expressed during leaf, spike and seed development. The expression patterns of individual members of the IPT, CKX, ZOG, and GLU multigene families in wheat are shown to be tissue- and developmentally-specific. For instance, TaIPT2 and TaCKX1 were the most highly expressed family members during early seed development, with relative expression levels of up to 90- and 900-fold higher, respectively, than those in the lowest expressed samples. The expression of two cis-ZOG genes was sharply increased in older leaves, while an extremely high mRNA level of TaGLU1-1 was detected in young leaves. Key genes with tissue- and developmentally-specific expression have been identified which would be prime targets for genetic manipulation towards yield improvement in bread wheat breeding programmes, utilising TILLING and MAS strategies.

Co-ordinated voltage control of DFIG wind turbines in uninterrupted operation during grid faults

DEFF Research Database (Denmark)

Hansen, Anca Daniela; Michalke, G.; Sørensen, Poul Ejnar

2007-01-01

Emphasis in this article is on the design of a co-ordinated voltage control strategy for doubly fed induction generator (DFIG) wind turbines that enhances their capability to provide grid support during grid faults. In contrast to its very good performance in normal operation, the DFIG wind turbine...... concept is quite sensitive to grid faults and requires special power converter protection. The fault ride-through and grid support capabilities of the DFIG address therefore primarily the design of DFIG wind turbine control with special focus on power converter protection and voltage control issues....... A voltage control strategy is designed and implemented in this article, based on the idea that both converters of the DFIG (i.e. rotor-side converter and grid-side converter) participate in the grid voltage control in a co-ordinated manner. By default the grid voltage is controlled by the rotor...

Spherical polar co-ordinate calculations of induced fields in the retina and head for applied magnetic fields at 50 Hz.

Science.gov (United States)

Dimbylow, Peter

2011-07-21

This paper sets out to explore the effects of voxel resolution, from 2 mm down to 0.1 mm for Cartesian co-ordinates and the differences between Cartesian and spherical polar co-ordinates for a standardized test-bed model of the eye. This model was taken from the work of Yoriyaz et al (2005 Radiat. Prot. Dosim. 115 316-9) who have developed a detailed geometric description of the eye including choroid, retina, sclera, lens, cornea, anterior chamber, vitreous humour and optic nerve for ophthalmic brachytherapy. The spherical co-ordinate model has radial and angular steplengths of 0.1 mm and 0.25°, respectively. The current density averaged over 1 cm(2) and the 99th percentile value of the induced electric field have been calculated in the retina and central nervous system for uniform magnetic fields. The Cartesian co-ordinate calculations proceed in a sequence of grids at 2, 1, 0.5, 0.2 and 0.1 mm resolution with the potentials from the previous calculation at a coarser grid providing the boundary conditions on the finer grid. The 0.2 mm grid provides the boundary conditions for the spherical polar calculations. Comparisons are made with the International Commission on Non-Ionizing Radiation Protection reference levels.

Spherical polar co-ordinate calculations of induced fields in the retina and head for applied magnetic fields at 50 Hz

International Nuclear Information System (INIS)

Dimbylow, Peter

2011-01-01

This paper sets out to explore the effects of voxel resolution, from 2 mm down to 0.1 mm for Cartesian co-ordinates and the differences between Cartesian and spherical polar co-ordinates for a standardized test-bed model of the eye. This model was taken from the work of Yoriyaz et al (2005 Radiat. Prot. Dosim. 115 316-9) who have developed a detailed geometric description of the eye including choroid, retina, sclera, lens, cornea, anterior chamber, vitreous humour and optic nerve for ophthalmic brachytherapy. The spherical co-ordinate model has radial and angular steplengths of 0.1 mm and 0.25 0 , respectively. The current density averaged over 1 cm 2 and the 99th percentile value of the induced electric field have been calculated in the retina and central nervous system for uniform magnetic fields. The Cartesian co-ordinate calculations proceed in a sequence of grids at 2, 1, 0.5, 0.2 and 0.1 mm resolution with the potentials from the previous calculation at a coarser grid providing the boundary conditions on the finer grid. The 0.2 mm grid provides the boundary conditions for the spherical polar calculations. Comparisons are made with the International Commission on Non-Ionizing Radiation Protection reference levels.

Analysis of Temporal-spatial Co-variation within Gene Expression Microarray Data in an Organogenesis Model

Science.gov (United States)

Ehler, Martin; Rajapakse, Vinodh; Zeeberg, Barry; Brooks, Brian; Brown, Jacob; Czaja, Wojciech; Bonner, Robert F.

The gene networks underlying closure of the optic fissure during vertebrate eye development are poorly understood. We used a novel clustering method based on Laplacian Eigenmaps, a nonlinear dimension reduction method, to analyze microarray data from laser capture microdissected (LCM) cells at the site and developmental stages (days 10.5 to 12.5) of optic fissure closure. Our new method provided greater biological specificity than classical clustering algorithms in terms of identifying more biological processes and functions related to eye development as defined by Gene Ontology at lower false discovery rates. This new methodology builds on the advantages of LCM to isolate pure phenotypic populations within complex tissues and allows improved ability to identify critical gene products expressed at lower copy number. The combination of LCM of embryonic organs, gene expression microarrays, and extracting spatial and temporal co-variations appear to be a powerful approach to understanding the gene regulatory networks that specify mammalian organogenesis.

Co-ordinate expression of glycine betaine synthesis genes linked by the FMDV 2A region in a single open reading frame in Pichia pastoris.

Science.gov (United States)

Wang, Sanhong; Yao, Quanhong; Tao, Jianmin; Qiao, Yushan; Zhang, Zhen

2007-12-01

The genes encoding the two enzymes choline monooxygenase (CMO) and betaine aldehyde dehydrogenase (BADH) of glycine betaine synthesis in Suaeda salsa were cloned and fused with the 2A region of foot-and-mouth disease virus in a single open reading frame. The fused genes were placed under the control of the alcohol oxidase (AOX1) promoter in pPIC3B and transformed into P. pastoris GS115. The expression of the fused genes in P. pastoris and the ability of recombinant yeasts to tolerate environmental stresses were studied. The results showed that induced with 0.5% methanol for 96 h, the maximal activities of CMO and BADH in the tested recombinant yeasts were 45- and 44-fold higher than those in the control yeast transformed empty vector only, respectively; the content of glycine betaine in the recombinant yeasts was 28- to 35-fold higher than that in the control. The fused genes linked by 2A region of foot-and-mouth disease virus were expressed in P. pastoris successfully and the polyprotein was 'cleaved' to each functional protein. The yeasts transformed the fused genes, which were more resistant to salt, methanol, and high temperature stresses than the control as result of glycine betaine synthesis genes introduced.

Educating Leaders for Social Justice: The Case of Special Educational Needs Co-Ordinators

Science.gov (United States)

Liasidou, Anastasia; Svensson, Cathy

2014-01-01

In the light of policy imperatives to initiate and maintain inclusive education reforms, the role of special educational needs co-ordinators (SENCOs) in England and Wales should be reconceptualised with a view to their leading school reforms commensurate with the principles of an inclusive discourse. The article concentrates on the social justice…

Genome-wide targeted prediction of ABA responsive genes in rice based on over-represented cis-motif in co-expressed genes.

Science.gov (United States)

Lenka, Sangram K; Lohia, Bikash; Kumar, Abhay; Chinnusamy, Viswanathan; Bansal, Kailash C

2009-02-01

Abscisic acid (ABA), the popular plant stress hormone, plays a key role in regulation of sub-set of stress responsive genes. These genes respond to ABA through specific transcription factors which bind to cis-regulatory elements present in their promoters. We discovered the ABA Responsive Element (ABRE) core (ACGT) containing CGMCACGTGB motif as over-represented motif among the promoters of ABA responsive co-expressed genes in rice. Targeted gene prediction strategy using this motif led to the identification of 402 protein coding genes potentially regulated by ABA-dependent molecular genetic network. RT-PCR analysis of arbitrarily chosen 45 genes from the predicted 402 genes confirmed 80% accuracy of our prediction. Plant Gene Ontology (GO) analysis of ABA responsive genes showed enrichment of signal transduction and stress related genes among diverse functional categories.

3. IAEA research co-ordination meeting on atomic and plasma-wall interaction data for fusion reactor divertor modeling. Summary report

International Nuclear Information System (INIS)

Janev, R.K.

1999-04-01

A brief description of the proceedings and the conclusions of the 3rd Research Co-ordination Meeting on 'Atomic and Plasma-Wall Interaction Data for Fusion Reactor Divertor Modeling', held on March 8-9, 1999, at the IAEA Headquarters in Vienna, Austria, is provided. The reports on the activities within the individual projects pertinent to the IAEA Co-ordinated Research program with the same title are given as appendix to the present report. (author)

Dynamic sporulation gene co-expression networks for Bacillus subtilis 168 and the food-borne isolate Bacillus amyloliquefaciens: a transcriptomic model.

Science.gov (United States)

Omony, Jimmy; de Jong, Anne; Krawczyk, Antonina O; Eijlander, Robyn T; Kuipers, Oscar P

2018-02-09

Sporulation is a survival strategy, adapted by bacterial cells in response to harsh environmental adversities. The adaptation potential differs between strains and the variations may arise from differences in gene regulation. Gene networks are a valuable way of studying such regulation processes and establishing associations between genes. We reconstructed and compared sporulation gene co-expression networks (GCNs) of the model laboratory strain Bacillus subtilis 168 and the food-borne industrial isolate Bacillus amyloliquefaciens. Transcriptome data obtained from samples of six stages during the sporulation process were used for network inference. Subsequently, a gene set enrichment analysis was performed to compare the reconstructed GCNs of B. subtilis 168 and B. amyloliquefaciens with respect to biological functions, which showed the enriched modules with coherent functional groups associated with sporulation. On basis of the GCNs and time-evolution of differentially expressed genes, we could identify novel candidate genes strongly associated with sporulation in B. subtilis 168 and B. amyloliquefaciens. The GCNs offer a framework for exploring transcription factors, their targets, and co-expressed genes during sporulation. Furthermore, the methodology described here can conveniently be applied to other species or biological processes.

Comparative modular analysis of gene expression in vertebrate organs

Directory of Open Access Journals (Sweden)

Piasecka Barbara

2012-03-01

Full Text Available Abstract Background The degree of conservation of gene expression between homologous organs largely remains an open question. Several recent studies reported some evidence in favor of such conservation. Most studies compute organs' similarity across all orthologous genes, whereas the expression level of many genes are not informative about organ specificity. Results Here, we use a modularization algorithm to overcome this limitation through the identification of inter-species co-modules of organs and genes. We identify such co-modules using mouse and human microarray expression data. They are functionally coherent both in terms of genes and of organs from both organisms. We show that a large proportion of genes belonging to the same co-module are orthologous between mouse and human. Moreover, their zebrafish orthologs also tend to be expressed in the corresponding homologous organs. Notable exceptions to the general pattern of conservation are the testis and the olfactory bulb. Interestingly, some co-modules consist of single organs, while others combine several functionally related organs. For instance, amygdala, cerebral cortex, hypothalamus and spinal cord form a clearly discernible unit of expression, both in mouse and human. Conclusions Our study provides a new framework for comparative analysis which will be applicable also to other sets of large-scale phenotypic data collected across different species.

Comparative modular analysis of gene expression in vertebrate organs.

Science.gov (United States)

Piasecka, Barbara; Kutalik, Zoltán; Roux, Julien; Bergmann, Sven; Robinson-Rechavi, Marc

2012-03-29

The degree of conservation of gene expression between homologous organs largely remains an open question. Several recent studies reported some evidence in favor of such conservation. Most studies compute organs' similarity across all orthologous genes, whereas the expression level of many genes are not informative about organ specificity. Here, we use a modularization algorithm to overcome this limitation through the identification of inter-species co-modules of organs and genes. We identify such co-modules using mouse and human microarray expression data. They are functionally coherent both in terms of genes and of organs from both organisms. We show that a large proportion of genes belonging to the same co-module are orthologous between mouse and human. Moreover, their zebrafish orthologs also tend to be expressed in the corresponding homologous organs. Notable exceptions to the general pattern of conservation are the testis and the olfactory bulb. Interestingly, some co-modules consist of single organs, while others combine several functionally related organs. For instance, amygdala, cerebral cortex, hypothalamus and spinal cord form a clearly discernible unit of expression, both in mouse and human. Our study provides a new framework for comparative analysis which will be applicable also to other sets of large-scale phenotypic data collected across different species.

Matrix factorization reveals aging-specific co-expression gene modules in the fat and muscle tissues in nonhuman primates

Science.gov (United States)

Wang, Yongcui; Zhao, Weiling; Zhou, Xiaobo

2016-10-01

Accurate identification of coherent transcriptional modules (subnetworks) in adipose and muscle tissues is important for revealing the related mechanisms and co-regulated pathways involved in the development of aging-related diseases. Here, we proposed a systematically computational approach, called ICEGM, to Identify the Co-Expression Gene Modules through a novel mathematical framework of Higher-Order Generalized Singular Value Decomposition (HO-GSVD). ICEGM was applied on the adipose, and heart and skeletal muscle tissues in old and young female African green vervet monkeys. The genes associated with the development of inflammation, cardiovascular and skeletal disorder diseases, and cancer were revealed by the ICEGM. Meanwhile, genes in the ICEGM modules were also enriched in the adipocytes, smooth muscle cells, cardiac myocytes, and immune cells. Comprehensive disease annotation and canonical pathway analysis indicated that immune cells, adipocytes, cardiomyocytes, and smooth muscle cells played a synergistic role in cardiac and physical functions in the aged monkeys by regulation of the biological processes associated with metabolism, inflammation, and atherosclerosis. In conclusion, the ICEGM provides an efficiently systematic framework for decoding the co-expression gene modules in multiple tissues. Analysis of genes in the ICEGM module yielded important insights on the cooperative role of multiple tissues in the development of diseases.

Organization of the ITER Co-ordinated Technical Activities International Team

International Nuclear Information System (INIS)

2001-01-01

At its meeting in Toronto on 7 November 2001, the ITER Co-ordinated Technical Activities (CTA) project board took note of the organizational arrangements for the CTA International Team at the Garching and Naka joint work sites. The organization chart of the team remains almost unchanged from that of the ITER Engineering Design Activities (EDA). However, there is no special division responsible for plasma and field control. Activities in plasma control will be taken over by the Physics Unit. This newsletter also includes the ITER CTA International Team structure

Use of isotope techniques in lake dynamics investigations. Proceedings of a final research co-ordination meeting

International Nuclear Information System (INIS)

2001-03-01

The Co-ordinated Research Programme (CRP) on the Use of Isotope Techniques in Lake Dynamics Investigations was launched with the aim of assessing the potential of environmental isotope techniques in studying the dynamics of surface water bodies and related problems such as: dynamics of solutes; sediment focusing; establishment of water balance components; vulnerability to pollution. The CRP enabled a number of isotope and geochemical studies to be carried out on small and large water bodies, with the general aim of understanding of the dynamics of these systems under the growing anthropogenic influence. This publication is a compilation of the papers presented at the final Research Co-ordination Meeting (RCM) held in Rehovot, Israel, from 10 to 13 March 1997. Individual contributions have been indexed separately

2. IAEA research co-ordination meeting on 'Data for molecular processes in edge plasmas'. Summary report

International Nuclear Information System (INIS)

Clark, R.E.H.

2004-05-01

This report briefly describes the proceedings, conclusions and recommendations of the 2nd Research Co-ordination Meeting (RCM) of the Co-ordinated Research Project (CRP) on 'Data for Molecular Processes in Edge Plasmas' held on 12-14 May 2003 at IAEA Headquarters, Vienna. During the course of the meeting the progress achieved to data was thoroughly reviewed. During the course of the meeting many areas in need of further research were noted. In addition there are specific important processes with lingering discrepancies between theory and experiment. Strong collaborations built during the course of this CRP have the potential to address these issues. Therefore, one outcome of the RCM was a detailed proposal to extend the CRP for an additional year with a final RCM in 2004. (author)

Step-by-Step Construction of Gene Co-expression Networks from High-Throughput Arabidopsis RNA Sequencing Data.

Science.gov (United States)

Contreras-López, Orlando; Moyano, Tomás C; Soto, Daniela C; Gutiérrez, Rodrigo A

2018-01-01

The rapid increase in the availability of transcriptomics data generated by RNA sequencing represents both a challenge and an opportunity for biologists without bioinformatics training. The challenge is handling, integrating, and interpreting these data sets. The opportunity is to use this information to generate testable hypothesis to understand molecular mechanisms controlling gene expression and biological processes (Fig. 1). A successful strategy to generate tractable hypotheses from transcriptomics data has been to build undirected network graphs based on patterns of gene co-expression. Many examples of new hypothesis derived from network analyses can be found in the literature, spanning different organisms including plants and specific fields such as root developmental biology.In order to make the process of constructing a gene co-expression network more accessible to biologists, here we provide step-by-step instructions using published RNA-seq experimental data obtained from a public database. Similar strategies have been used in previous studies to advance root developmental biology. This guide includes basic instructions for the operation of widely used open source platforms such as Bio-Linux, R, and Cytoscape. Even though the data we used in this example was obtained from Arabidopsis thaliana, the workflow developed in this guide can be easily adapted to work with RNA-seq data from any organism.

Associations of motor co-ordination and attention with motor-perceptual development in 3-year-old preterm and full-term children who needed neonatal intensive care.

Science.gov (United States)

Hemgren, E; Persson, K

2007-01-01

Children who have needed neonatal intensive care (NIC) are considered to be at risk for deficits such as developmental co-ordination disorder and attention-deficit/hyperactivity disorder. By assessing motor-perceptual development, motor co-ordination and attention already at 3 years of age, it might be possible to identify such deficits earlier than they are today. To investigate the motor-perceptual development in a group of 202 NIC children but had no major impairments, to describe associations of deficits in co-ordination and attention with motor-perceptual delays, and to estimate the prevalence of NIC children with combined deficits together with a motor-perceptual delay. Co-ordination and attention in children born very preterm (n = 57), moderately preterm (n = 75) and full-term (n = 70) were observed according to a model for Combined Assessment of Motor Performance and Behaviour while they were assessed using a developmental scale, Motor-Perceptual Development, 0-7 years, MPU. In two out of 14 MPU areas, a larger proportion of very preterm than of moderately preterm and full-term children had marked developmental delay. Overall, the proportion of NIC children having a motor-perceptual delay increased with increasing incoordination and especially increasing lack of attention. Twenty-one (11%) of the NIC children had different motor-perceptual delays combined with pronounced incoordination and pronounced lack of attention. Deficits in co-ordination and attention were associated with motor-perceptual delays in areas important for daily living and development of academic skills. Therefore, to find children at risk for developmental co-ordination disorder and attention-deficit/hyperactivity disorder, assessments of co-ordination and attention should be added to assessments of motor-perceptual development in 3-year-old NIC children.

Use of mutation techniques for improvement of cereals in Latin America. Final reports of a co-ordinated research programme

Energy Technology Data Exchange (ETDEWEB)

NONE

1996-01-01

This publication presents the scientific results obtained under the FAO/IAEA Co-ordinated Research Programme on Improvement of Cereals in Latin America through Mutation Breeding. Some of the selected mutants were already tested in multilocation trials and had higher yields and/or other advantages, in comparison with the leading local varieties. On the basis of these results it it expected that a few new mutant varieties of rice (Brazil, Costa Rica, Cuba, Guatemala), wheat (Brazil, Chile) and barley (Peru) will be officially released within the next few years. Still more mutants, which are valuable for conventional breeding programmes as new sources of desired genes, were selected. Refs, figs and tabs.

Drought controls on H2O2 accumulation, catalase (CAT) activity and CAT gene expression in wheat.

Science.gov (United States)

Luna, Celina M; Pastori, Gabriela M; Driscoll, Simon; Groten, Karin; Bernard, Stephanie; Foyer, Christine H

2005-01-01

Plants co-ordinate information derived from many diverse external and internal signals to ensure appropriate control of gene expression under optimal and stress conditions. In this work, the relationships between catalase (CAT) and H2O2 during drought in wheat (Triticum aestivum L.) are studied. Drought-induced H2O2 accumulation correlated with decreases in soil water content and CO2 assimilation. Leaf H2O2 content increased even though total CAT activity doubled under severe drought conditions. Diurnal regulation of CAT1 and CAT2 mRNA abundance was apparent in all conditions and day/night CAT1 and CAT2 expression patterns were modified by mild and severe drought. The abundance of CAT1 transcripts was regulated by circadian controls that persisted in continuous darkness, while CAT2 was modulated by light. Drought decreased abundance, and modified the pattern, of CAT1 and CAT2 mRNAs. It was concluded that the complex regulation of CAT mRNA, particularly at the level of translation, allows precise control of leaf H2O2 accumulation.

The duplicated genes database: identification and functional annotation of co-localised duplicated genes across genomes.

Directory of Open Access Journals (Sweden)

Marion Ouedraogo

Full Text Available BACKGROUND: There has been a surge in studies linking genome structure and gene expression, with special focus on duplicated genes. Although initially duplicated from the same sequence, duplicated genes can diverge strongly over evolution and take on different functions or regulated expression. However, information on the function and expression of duplicated genes remains sparse. Identifying groups of duplicated genes in different genomes and characterizing their expression and function would therefore be of great interest to the research community. The 'Duplicated Genes Database' (DGD was developed for this purpose. METHODOLOGY: Nine species were included in the DGD. For each species, BLAST analyses were conducted on peptide sequences corresponding to the genes mapped on a same chromosome. Groups of duplicated genes were defined based on these pairwise BLAST comparisons and the genomic location of the genes. For each group, Pearson correlations between gene expression data and semantic similarities between functional GO annotations were also computed when the relevant information was available. CONCLUSIONS: The Duplicated Gene Database provides a list of co-localised and duplicated genes for several species with the available gene co-expression level and semantic similarity value of functional annotation. Adding these data to the groups of duplicated genes provides biological information that can prove useful to gene expression analyses. The Duplicated Gene Database can be freely accessed through the DGD website at http://dgd.genouest.org.

Co-expression of G2-EPSPS and glyphosate acetyltransferase GAT genes conferring high tolerance to glyphosate in soybean

Directory of Open Access Journals (Sweden)

Bingfu eGuo

2015-10-01

Full Text Available Glyphosate is a widely used non-selective herbicide with broad spectrum of weed control around the world. At present, most of the commercial glyphosate tolerant soybeans utilize glyphosate tolerant gene CP4-EPSPS or glyphosate acetyltransferase gene GAT separately. In this study, both glyphosate tolerant gene G2-EPSPS and glyphosate degraded gene GAT were co-transferred into soybean and transgenic plants showed high tolerance to glyphosate. Molecular analysis including PCR, Sothern blot, qRT-PCR and Western blot revealed that target genes have been integrated into genome and expressed effectively at both mRNA and protein levels. Furthermore, the glyphosate tolerance analysis showed that no typical symptom was observed when compared with a glyphosate tolerant line HJ06-698 derived from GR1 transgenic soybean even at four-fold labeled rate of Roundup. Chlorophyll and shikimic acid content analysis of transgenic plant also revealed that these two indexes were not significantly altered after glyphosate application. These results indicated that co-expression of G2-EPSPS and GAT conferred high tolerance to the herbicide glyphosate in soybean. Therefore, combination of tolerant and degraded genes provides a new strategy for developing glyphosate tolerant transgenic crops.

Utility and Limitations of Using Gene Expression Data to Identify Functional Associations.

Directory of Open Access Journals (Sweden)

Sahra Uygun

2016-12-01

Full Text Available Gene co-expression has been widely used to hypothesize gene function through guilt-by association. However, it is not clear to what degree co-expression is informative, whether it can be applied to genes involved in different biological processes, and how the type of dataset impacts inferences about gene functions. Here our goal is to assess the utility and limitations of using co-expression as a criterion to recover functional associations between genes. By determining the percentage of gene pairs in a metabolic pathway with significant expression correlation, we found that many genes in the same pathway do not have similar transcript profiles and the choice of dataset, annotation quality, gene function, expression similarity measure, and clustering approach significantly impacts the ability to recover functional associations between genes using Arabidopsis thaliana as an example. Some datasets are more informative in capturing coordinated expression profiles and larger data sets are not always better. In addition, to recover the maximum number of known pathways and identify candidate genes with similar functions, it is important to explore rather exhaustively multiple dataset combinations, similarity measures, clustering algorithms and parameters. Finally, we validated the biological relevance of co-expression cluster memberships with an independent phenomics dataset and found that genes that consistently cluster with leucine degradation genes tend to have similar leucine levels in mutants. This study provides a framework for obtaining gene functional associations by maximizing the information that can be obtained from gene expression datasets.

Radiation doses in diagnostic radiology and methods for dose reduction. Report of a co-ordinated research programme (1991-1993)

Energy Technology Data Exchange (ETDEWEB)

NONE

1995-04-01

It is well recognized that diagnostic radiology is the largest contributor to the collective dose from all man-made sources of radiation. Large differences in radiation doses from the same procedures among different X ray rooms have led to the conclusion that there is a potential for dose reduction. A Co-ordinated Research Programme on Radiation Doses in Diagnostic Radiology and Methods for Dose Reduction, involving Member States with different degrees of development, was launched by the IAEA in co-operation with the CEC. This report summarizes the results of the second and final Research Co-ordination Meeting held in Vienna from 4 to 8 October 1993. 22 refs, 6 figs and tabs.

Radiation doses in diagnostic radiology and methods for dose reduction. Report of a co-ordinated research programme (1991-1993)

International Nuclear Information System (INIS)

1995-04-01

It is well recognized that diagnostic radiology is the largest contributor to the collective dose from all man-made sources of radiation. Large differences in radiation doses from the same procedures among different X ray rooms have led to the conclusion that there is a potential for dose reduction. A Co-ordinated Research Programme on Radiation Doses in Diagnostic Radiology and Methods for Dose Reduction, involving Member States with different degrees of development, was launched by the IAEA in co-operation with the CEC. This report summarizes the results of the second and final Research Co-ordination Meeting held in Vienna from 4 to 8 October 1993. 22 refs, 6 figs and tabs

Co-ordinated research programme on nuclear techniques for toxic elements in foodstuffs

International Nuclear Information System (INIS)

1990-01-01

This Co-ordinated Research Programme (CRP) was started by the Agency in 1985, within the framework of the Regional Cooperative Agreement for Research, Development and Training Related to Nuclear Science and Technology in the Asia and Pacific Region (RCA). Its main purpose has been to obtain comparative data on existing elemental concentrations of potentially toxic elements in foodstuffs in various Asian countries. The elements to be studied include the potentially most toxic trace elements (As, Cd, Hg, Pb, Se) as well as others of relevance to national monitoring programmes, such as Br, Cr, Cu, Fe, I, Mn, Sb, Tl, and Zn. An important supplementary purpose of the programme is to help establish analytical expertise for work of this kind in the individual countries. Scientists from several RCA Member States have participated in it, namely from Australia, Bangladesh, China, India, Indonesia, Japan, Malaysia, Pakistan, Thailand, and also from institutes in several countries outside the region, i.e., Argentina, Brazil, Jamaica and The Netherlands. This report summarizes the discussions that took place during the third and final Research Co-ordination Meeting (RCM) for the programme from 20-24 November 1989, in Jakarta, Indonesia. This document includes the progress reports presented by the participants as well as discussions and conclusions drawn from the meeting

Loss of co-ordinate expression of progesterone receptors A and B is an early event in breast carcinogenesis.

Science.gov (United States)

Mote, P A; Bartow, S; Tran, N; Clarke, C L

2002-03-01

Progesterone receptor (PR) mediates the effects of progesterone in mammary tissues and plays a crucial role in normal breast development and in breast cancer. PR proteins are expressed as two isoforms, PRA and PRB, that have different capacities to activate target genes, yet it is unknown whether progesterone action in normal and malignant breast is mediated by PRA and/or PRB. This study determines the relative expression of PRA and PRB in normal breast and in benign, premalignant and malignant archival breast lesions by dual immunofluorescent histochemistry. In normal breast and in proliferative disease without atypia (PDWA) PRA and PRB were co-expressed within the same cells in comparable amounts, implicating both isoforms in progesterone action. In atypical lesions, however, there was a significant increase in predominant expression of PRA or PRB, with lesion progression from the normal state to malignancy. PR isoform predominance, especially PRA predominance, was evident in a high proportion of ductal carcinomas in situ (DCIS) and invasive breast lesions. In the normal breast and in PDWA, the relative expression of PRA and PRB in adjacent cells was homogenous. There was a significant increase in cell-to-cell heterogeneity of PR isoform expression in ADH and DCIS lesions and in the majority of breast cancers. Heterogeneous cell-to-cell expression of PR isoforms occurred prior to overall predominant expression of one isoform in premalignant breast lesions, demonstrating that loss of control of relative PRA:PRB expression is an early event in the development of breast cancer. PRA:PRB ratios within a breast lesion are likely to be important as both markers and effectors of tumor growth and development, and progressively aberrant PR isoform expression may play a role in the etiology of breast cancer.

Identifying miRNA and gene modules of colon cancer associated with pathological stage by weighted gene co-expression network analysis

Directory of Open Access Journals (Sweden)

Zhou X

2018-05-01

Full Text Available Xian-guo Zhou,1,2,* Xiao-liang Huang,1,2,* Si-yuan Liang,1–3 Shao-mei Tang,1,2 Si-kao Wu,1,2 Tong-tong Huang,1,2 Zeng-nan Mo,1,2,4 Qiu-yan Wang1,2,5 1Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People’s Republic of China; 2Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, Guangxi Zhuang Autonomous Region, People’s Republic of China; 3Department of Colorectal Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People’s Republic of China; 4Department of Urology and Nephrology, The First Affiliated Hospital of Guangxi, Medical University, Nanning, Guangxi Zhuang Autonomous Region, People’s Republic of China; 5Guangxi Colleges and Universities Key Laboratory of Biological Molecular Medicine Research, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People’s Republic of China *These authors contributed equally to this work Introduction: Colorectal cancer (CRC is the fourth most common cause of cancer-related mortality worldwide. The tumor, node, metastasis (TNM stage remains the standard for CRC prognostication. Identification of meaningful microRNA (miRNA and gene modules or representative biomarkers related to the pathological stage of colon cancer helps to predict prognosis and reveal the mechanisms behind cancer progression.Materials and methods: We applied a systems biology approach by combining differential expression analysis and weighted gene co-expression network analysis (WGCNA to detect the pathological stage-related miRNA and gene modules and construct a miRNA–gene network. The Cancer Genome Atlas (TCGA colon adenocarcinoma (CAC RNA-sequencing data and miRNA-sequencing data were subjected to WGCNA analysis, and the GSE29623, GSE35602 and GSE39396 were utilized to validate and

2nd (final) IAEA research co-ordination meeting on 'charge exchange cross section data for fusion plasma studies'. Summary report

International Nuclear Information System (INIS)

Clark, R.E.H.

2001-11-01

The proceedings and conclusions of the 2nd Research Co-ordination Meeting on 'Charge Exchange Cross Section Data for Fusion Plasma Studies', held on September 25 and 26, 2000 at the IAEA Headquarters in Vienna, are briefly described. This report includes a summary of the presentations made by the meeting participants and a review of the accomplishments of the Co-ordinated Research Project (CRP). In addition, short summaries from the participants are included indicating the specific research completed in support of this CRP. (author)

Comparative gene expression between two yeast species

Directory of Open Access Journals (Sweden)

Guan Yuanfang

2013-01-01

Full Text Available Abstract Background Comparative genomics brings insight into sequence evolution, but even more may be learned by coupling sequence analyses with experimental tests of gene function and regulation. However, the reliability of such comparisons is often limited by biased sampling of expression conditions and incomplete knowledge of gene functions across species. To address these challenges, we previously systematically generated expression profiles in Saccharomyces bayanus to maximize functional coverage as compared to an existing Saccharomyces cerevisiae data repository. Results In this paper, we take advantage of these two data repositories to compare patterns of ortholog expression in a wide variety of conditions. First, we developed a scalable metric for expression divergence that enabled us to detect a significant correlation between sequence and expression conservation on the global level, which previous smaller-scale expression studies failed to detect. Despite this global conservation trend, between-species gene expression neighborhoods were less well-conserved than within-species comparisons across different environmental perturbations, and approximately 4% of orthologs exhibited a significant change in co-expression partners. Furthermore, our analysis of matched perturbations collected in both species (such as diauxic shift and cell cycle synchrony demonstrated that approximately a quarter of orthologs exhibit condition-specific expression pattern differences. Conclusions Taken together, these analyses provide a global view of gene expression patterns between two species, both in terms of the conditions and timing of a gene's expression as well as co-expression partners. Our results provide testable hypotheses that will direct future experiments to determine how these changes may be specified in the genome.

Early bovine embryos regulate oviduct epithelial cell gene expression during in vitro co-culture.

Science.gov (United States)

Schmaltz-Panneau, Barbara; Cordova, Amanda; Dhorne-Pollet, Sophie; Hennequet-Antier, Christelle; Uzbekova, Sveltlana; Martinot, Emmanuelle; Doret, Sarah; Martin, Patrice; Mermillod, Pascal; Locatelli, Yann

2014-10-01

In mammals, the oviduct may participate to the regulation of early embryo development. In vitro co-culture of early bovine embryos with bovine oviduct epithelial cells (BOEC) has been largely used to mimic the maternal environment. However, the mechanisms of BOEC action have not been clearly elucidated yet. The aim of this study was to determine the response of BOEC cultures to the presence of developing bovine embryos. A 21,581-element bovine oligonucleotide array was used compare the gene expression profiles of confluent BOEC cultured for 8 days with or without embryos. This study revealed 34 differentially expressed genes (DEG). Of these 34 genes, IFI6, ISG15, MX1, IFI27, IFI44, RSAD2, IFITM1, EPSTI1, USP18, IFIT5, and STAT1 expression increased to the greatest extent due to the presence of embryos with a major impact on antiviral and immune response. Among the mRNAs at least 25 are already described as induced by interferons. In addition, transcript levels of new candidate genes involved in the regulation of transcription, modulation of the maternal immune system and endometrial remodeling were found to be increased. We selected 7 genes and confirmed their differential expression by quantitative RT-PCR. The immunofluorescence imaging of cellular localization of STAT1 protein in BOEC showed a nuclear translocation in the presence of embryos, suggesting the activation of interferon signaling pathway. This first systematic study of BOEC transcriptome changes in response to the presence of embryos in cattle provides some evidences that these cells are able to adapt their transcriptomic profile in response to embryo signaling. Copyright © 2014 Elsevier B.V. All rights reserved.

Co-ordinated research project on validation and application of plants as biomonitors of trace element atmospheric pollution, analysed by nuclear and related techniques. Report on the 1. research co-ordination meeting

Energy Technology Data Exchange (ETDEWEB)

NONE

1999-07-01

Environmental pollution is a cause of ever increasing concern in the world. The UN Conference on Environment and Development (Rio, Brazil, 1992) reaffirmed the importance of protecting the environment within the context of sustainable development. Arising out of this conference, the Rio Agenda 21 declaration called for a number of nationally determined action programmes, with international assistance and co-ordination under 'Capacity 21', concerning environmental monitoring and assessment, including the use of biological markers. Environmental protection and control is a matter of high priority in all developing countries' governmental policies in view of its implications for the welfare of the present and future populations. Therefore it is expected that regional and national organisations responsible for legislation and environmental policy, municipal organisations, which could use the data collected for establishing emission levels, organisations responsible for pollutant emission control and public health-related institutions will benefit from this proposed Co-ordinated Research Project (CRP). The CRP is expected to exploit possibilities of developing and validating tools for using appropriate biomonitors to map the distribution of air pollution over wide areas in developing countries. If successful, this would be a powerful way for developing countries to monitor air pollution.

Co-ordinated research project on validation and application of plants as biomonitors of trace element atmospheric pollution, analysed by nuclear and related techniques. Report on the 1. research co-ordination meeting

International Nuclear Information System (INIS)

1999-01-01

Environmental pollution is a cause of ever increasing concern in the world. The UN Conference on Environment and Development (Rio, Brazil, 1992) reaffirmed the importance of protecting the environment within the context of sustainable development. Arising out of this conference, the Rio Agenda 21 declaration called for a number of nationally determined action programmes, with international assistance and co-ordination under 'Capacity 21', concerning environmental monitoring and assessment, including the use of biological markers. Environmental protection and control is a matter of high priority in all developing countries' governmental policies in view of its implications for the welfare of the present and future populations. Therefore it is expected that regional and national organisations responsible for legislation and environmental policy, municipal organisations, which could use the data collected for establishing emission levels, organisations responsible for pollutant emission control and public health-related institutions will benefit from this proposed Co-ordinated Research Project (CRP). The CRP is expected to exploit possibilities of developing and validating tools for using appropriate biomonitors to map the distribution of air pollution over wide areas in developing countries. If successful, this would be a powerful way for developing countries to monitor air pollution

Ethylene-Related Gene Expression Networks in Wood Formation

Directory of Open Access Journals (Sweden)

Carolin Seyfferth

2018-03-01

Full Text Available Thickening of tree stems is the result of secondary growth, accomplished by the meristematic activity of the vascular cambium. Secondary growth of the stem entails developmental cascades resulting in the formation of secondary phloem outwards and secondary xylem (i.e., wood inwards of the stem. Signaling and transcriptional reprogramming by the phytohormone ethylene modifies cambial growth and cell differentiation, but the molecular link between ethylene and secondary growth remains unknown. We addressed this shortcoming by analyzing expression profiles and co-expression networks of ethylene pathway genes using the AspWood transcriptome database which covers all stages of secondary growth in aspen (Populus tremula stems. ACC synthase expression suggests that the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC is synthesized during xylem expansion and xylem cell maturation. Ethylene-mediated transcriptional reprogramming occurs during all stages of secondary growth, as deduced from AspWood expression profiles of ethylene-responsive genes. A network centrality analysis of the AspWood dataset identified EIN3D and 11 ERFs as hubs. No overlap was found between the co-expressed genes of the EIN3 and ERF hubs, suggesting target diversification and hence independent roles for these transcription factor families during normal wood formation. The EIN3D hub was part of a large co-expression gene module, which contained 16 transcription factors, among them several new candidates that have not been earlier connected to wood formation and a VND-INTERACTING 2 (VNI2 homolog. We experimentally demonstrated Populus EIN3D function in ethylene signaling in Arabidopsis thaliana. The ERF hubs ERF118 and ERF119 were connected on the basis of their expression pattern and gene co-expression module composition to xylem cell expansion and secondary cell wall formation, respectively. We hereby establish data resources for ethylene-responsive genes and

Co-ordinated research programme on applications of stable isotope tracers in human nutrition research

International Nuclear Information System (INIS)

1989-01-01

This Co-ordinated Research Programme (CRP) was formally established by the Agency in October 1988, and has since then expanded to encompass 13 participants in 13 countries. Its general objective is to help establish competence in the use of stable isotope techniques, particularly in developing countries, and particularly with reference to applications of 2 H, 13 C, 15 N, and 18 O. This report summarizes the discussions that took place during the first Research Co-ordination Meeting (RCM). Working papers (progress reports) presented by the participants are included as annexes together with a preliminary report on the results of a series of intercomparison exercises involving enriched stable isotope reference materials containing 2 H, 13 C, 15 N and 18 O. For the future it was agreed that more work needs to be done to harmonize the analytical techniques being used, and to obtain support for new CRPs relating to human energy expenditure studies in pregnancy, lactation, growth and other conditions, and to studies of nitrogen turnover in relation to malnutrition and liver function. Refs, figs and tabs

A microscopic study of the S band in the generator co-ordinate approach

International Nuclear Information System (INIS)

Wuest, E.; Ansari, A.

1985-04-01

Using particle number and spin projected cranked Hartree-Fock-Bogolubov (CHFB) wave functions in the generator co-ordinate method (GCM) with the cranking frequency as a GC the shortcomings of the usual CHFB theory are removed and the ground as well as the s band are studied simultaneously. In particular, low-spin properties of the s band are discussed for a backbending nucleus 158 Dy. (author)

Production of 99Tcm radiopharmaceuticals for brain, heart and kidney imaging. Final report of a co-ordinated research programme 1991-1994

International Nuclear Information System (INIS)

1995-07-01

The report contains highlights of the achievements of the IAEA Co-ordinated Research programme on Evaluation on the Use of Bulk Reagents for the Production of 99 Tc m Radiopharmaceutical and Kits, the participants' summary reports (Argentina, Chile, Greece, India, Indonesia, Japan, Malaysia, Portugal, Russian Federation, Thailand, Uruguay, United States of America), recommended product protocols for five compounds and the participants' recommendations regarding continued support and further directions of co-ordinated research work. Refs, 6 figs, 8 tabs, 6 schemes

Co-ordinate changes in enzymes of fatty acid synthesis, activation and esterification in rabbit mammary gland druing pregnancy and lactation.

Science.gov (United States)

Short, V J; Brindley, D N; Dils, R

1977-01-01

1. The activities of fatty acid synthetase, acyl-CoA synthetase, glycerol phosphate acyltransferase and phosphatidate phosphatase were measured in the mammary glands of rabbits from day 16 of pregnancy to day 15 of post partum. 2. There were significant correlations between the increases in activities of these enzymes during this period. This was the case whether the activities were expressed per mg of homogenate protein, per g wet wt. of tissue or per total wet weight of the whole glands. The only exception was the lack of correlation between the activities of fatty acid synthetase and of phosphatidate phosphatase per g wet wt. of tissue. 3. These co-ordinate increases are discussed in relation to the changes which occur in fatty acid metabolism in the mammary gland during pregnancy and lactation. PMID:192226

Intercomparison and biokinetic model validation of radionuclide intake assessment. Report of a co-ordinated research project. 1996-1998

International Nuclear Information System (INIS)

1999-03-01

This TECDOC presents the results of a Co-ordinated Research Project (CRP) on Intercomparison and Biokinetic Model Validation of Radionuclide Intake Assessment, including the conclusions of a Research Co-ordination Meeting held from 6 to 8 July 1998. The present CRP on Intercomparison and Biokinetic Model Validation of Radionuclide Intake Assessment is part of the activities of the IAEA's Occupational Protection programme. The objective of this programme is to promote an internationally harmonized approach for optimizing occupational radiation protection through: the development of guides, within the IAEA's activities for establishing standards for radiation protection, for restricting radiation exposures in the workplace and for applying current occupational radiation protection techniques; and the promotion of application of these guidelines

Promotion of growth by Coenzyme Q10 is linked to gene expression in C. elegans.

Science.gov (United States)

Fischer, Alexandra; Niklowitz, Petra; Menke, Thomas; Döring, Frank

2014-10-03

Coenzyme Q (CoQ, ubiquinone) is an essential component of the respiratory chain, a cofactor of pyrimidine biosynthesis and acts as an antioxidant in extra mitochondrial membranes. More recently CoQ has been identified as a modulator of apoptosis, inflammation and gene expression. CoQ deficient Caenorhabditis elegans clk-1 mutants show several phenotypes including a delayed postembryonic growth. Using wild type and two clk-1 mutants, here we established an experimental set-up to study the consequences of endogenous CoQ deficiency or exogenous CoQ supply on gene expression and growth. We found that a deficiency of endogenous CoQ synthesis down-regulates a cluster of genes that are important for growth (i.e., RNA polymerase II, eukaryotic initiation factor) and up-regulates oxidation reactions (i.e., cytochrome P450, superoxide dismutase) and protein interactions (i.e., F-Box proteins). Exogenous CoQ supply partially restores the expression of these genes as well as the growth retardation of CoQ deficient clk-1 mutants. On the other hand exogenous CoQ supply does not alter the expression of a further sub-set of genes. These genes are involved in metabolism (i.e., succinate dehydrogenase complex), cell signalling or synthesis of lectins. Thus, our work provides a comprehensive overview of genes which can be modulated in their expression by endogenous or exogenous CoQ. As growth retardation in CoQ deficiency is linked to the gene expression profile we suggest that CoQ promotes growth via gene expression. Copyright © 2014 Elsevier Inc. All rights reserved.

Expression patterns of HvCKX genes indicate their role in growth and reproductive development of barley.

Directory of Open Access Journals (Sweden)

Wojciech Zalewski

Full Text Available Cytokinin oxidase/dehydrogenase proteins (CKX are encoded by a multigene family of CKX genes with a varying number of members depending on species. For some of the genes, spectacular effects on grain production in selected cereals have been observed. Despite the fact that partial or full length sequences of most HvCKX genes in barley (Hordeum vulgare have already been published, in most cases their specific biological functions have not been reported. Detailed expression patterns for five HvCKX genes in different organs/tissues of developing barley plants coupled with analysis of RNAi silent for two genes are presented to test the hypothesis that these expression profiles might indicate their function. Elevated expression for four of them - HvCKX1, HvCKX9, HvCKX4, and HvCKX11 - was found in developing kernels of wild-type plants compared to other tissues. HvCKX5 was mainly expressed in leaf tissue. Lower expression was noted for HvCKX1 in seedling roots and for HvCKX9 in leaves. The documented effect of RNAi silencing of HvCKX1 and a trend for HvCKX9 was higher plant productivity, and the trait was inherited through four generations. Higher plant yield was determined by higher numbers of seeds and spikes. Increased productivity was significantly greater in HvCKX1 silenced plants showing higher relative expression of HvCKX1 in developing kernels of wild-type plants compared to the expression of HvCKX9. Both HvCKX1 silenced T1 seedlings of cv. Golden Promise and the newly transformed breeding line STH7308 showed greater root mass, but this trait was not inherited in the next generation. Similarly HvCKX9 silenced T1 seedlings exhibited greater plant height without inheritance in the next generation. It is suggested that these effects were not inherited because of compensation by other genes co-ordinately regulating reproductive development. One line with untypically changed, inherited phenotype, which was selected from several dozen silenced lines

Construction and comparison of gene co-expression networks shows complex plant immune responses

Directory of Open Access Journals (Sweden)

Luis Guillermo Leal

2014-10-01

Full Text Available Gene co-expression networks (GCNs are graphic representations that depict the coordinated transcription of genes in response to certain stimuli. GCNs provide functional annotations of genes whose function is unknown and are further used in studies of translational functional genomics among species. In this work, a methodology for the reconstruction and comparison of GCNs is presented. This approach was applied using gene expression data that were obtained from immunity experiments in Arabidopsis thaliana, rice, soybean, tomato and cassava. After the evaluation of diverse similarity metrics for the GCN reconstruction, we recommended the mutual information coefficient measurement and a clustering coefficient-based method for similarity threshold selection. To compare GCNs, we proposed a multivariate approach based on the Principal Component Analysis (PCA. Branches of plant immunity that were exemplified by each experiment were analyzed in conjunction with the PCA results, suggesting both the robustness and the dynamic nature of the cellular responses. The dynamic of molecular plant responses produced networks with different characteristics that are differentiable using our methodology. The comparison of GCNs from plant pathosystems, showed that in response to similar pathogens plants could activate conserved signaling pathways. The results confirmed that the closeness of GCNs projected on the principal component space is an indicative of similarity among GCNs. This also can be used to understand global patterns of events triggered during plant immune responses.

GOBO: gene expression-based outcome for breast cancer online.

Directory of Open Access Journals (Sweden)

Markus Ringnér

Full Text Available Microarray-based gene expression analysis holds promise of improving prognostication and treatment decisions for breast cancer patients. However, the heterogeneity of breast cancer emphasizes the need for validation of prognostic gene signatures in larger sample sets stratified into relevant subgroups. Here, we describe a multifunctional user-friendly online tool, GOBO (http://co.bmc.lu.se/gobo, allowing a range of different analyses to be performed in an 1881-sample breast tumor data set, and a 51-sample breast cancer cell line set, both generated on Affymetrix U133A microarrays. GOBO supports a wide range of applications including: 1 rapid assessment of gene expression levels in subgroups of breast tumors and cell lines, 2 identification of co-expressed genes for creation of potential metagenes, 3 association with outcome for gene expression levels of single genes, sets of genes, or gene signatures in multiple subgroups of the 1881-sample breast cancer data set. The design and implementation of GOBO facilitate easy incorporation of additional query functions and applications, as well as additional data sets irrespective of tumor type and array platform.

The far and distal enhancers in the CYP3A4 gene co-ordinate the proximal promoter in responding similarly to the pregnane X receptor but differentially to hepatocyte nuclear factor-4alpha.

Science.gov (United States)

Liu, Fu-Jun; Song, Xiulong; Yang, Dongfang; Deng, Ruitang; Yan, Bingfang

2008-01-01

CYP3A4 (cytochrome P450 3A4) is involved in the metabolism of more than 50% of drugs and other xenobiotics. The expression of CYP3A4 is induced by many structurally dissimilar compounds. The PXR (pregnane X receptor) is recognized as a key regulator for the induction, and the PXR-directed transactivation of the CYP3A4 gene is achieved through a co-ordinated mechanism of the distal module with the proximal promoter. Recently, a far module was found to support constitutive expression of CYP3A4. The far module, like the distal module, is structurally clustered by a PXR response element (F-ER6) and elements recognized by HNF-4alpha (hepatocyte nuclear receptor-4alpha). We hypothesized that the far module supports PXR transactivation of the CYP3A4 gene. Consistent with the hypothesis, fusion of the far module to the proximal promoter of CYP3A4 markedly increased rifampicin-induced reporter activity. The increase was synergistically enhanced when both the far and distal modules were fused to the proximal promoter. The increase, however, was significantly reduced when the F-ER6 was disrupted. Chromatin immunoprecipitation detected the presence of PXR in the far module. Interestingly, HNF-4alpha increased the activity of the distal-proximal fused promoter, but decreased the activity of the far-proximal fused promoter. Given the fact that induction of CYP3A4 represents an important detoxification mechanism, the functional redundancy and synergistic interaction in supporting PXR transactivation suggest that the far and distal modules ensure the induction of CYP3A4 during chemical insults. The difference in responding to HNF-4alpha suggests that the magnitude of the induction is under control through various transcriptional networks.

2. IAEA research co-ordination meeting on 'Atomic and molecular data for fusion plasma diagnostics'. Summary report

International Nuclear Information System (INIS)

Clark, R.E.H.

2004-05-01

This report briefly describes the proceedings, conclusions and recommendations of the 2nd Research Co-ordination Meeting (RCM) of the Co-ordinated Research Project (CRP) on 'Atomic and Molecular Data for Fusion Plasma Diagnostics' held on 16-18 June 2003 at IAEA Headquarters, Vienna. During the course of the meeting the progress achieved to data was thoroughly reviewed. It was noted that during the course of the research several new areas of data needs were revealed. During detailed discussions proposals from all participants on ongoing data needs indicated that a one year extension of the CRP would be extremely valuable with an additional RCM to be held in 2004. A specific proposal for such an extension was formulated along with the summary of the results achieved to date. (author)

Chromium downregulates the expression of Acetyl CoA Carboxylase 1 gene in lipogenic tissues of domestic goats: a potential strategy for meat quality improvement.

Science.gov (United States)

Najafpanah, Mohammad Javad; Sadeghi, Mostafa; Zali, Abolfazl; Moradi-Shahrebabak, Hossein; Mousapour, Hojatollah

2014-06-15

Acetyl CoA Carboxylase 1 (ACC1) is a biotin-dependent enzyme that catalyzes the carboxylation of Acetyl CoA to form Malonyl CoA, the key intermediate metabolite in fatty acid synthesis. In this study, the mRNA expression of the ACC1 gene was evaluated in four different tissues (liver, visceral fat, subcutaneous fat, and longissimus muscle) of the domestic goat (Capra hircus) kids feeding on four different levels of trivalent chromium (0, 0.5, 1, and 1.5mg/day) as food supplementation. RT-qPCR technique was used for expression analyses and heat shock protein 90 gene (HSP-90) was considered as reference gene for data normalization. Our results revealed that 1.5mg/day chromium significantly reduced the expression of the ACC1 gene in liver, visceral fat, and subcutaneous fat tissues, but not in longissimus muscles (Pmeat quality in domestic animals. Copyright © 2014 Elsevier B.V. All rights reserved.

Radioactive waste management in Spain: co-ordination and projects

International Nuclear Information System (INIS)

2007-01-01

The sixth workshop of the OECD/NEA Forum on Stakeholder Confidence (FSC) was hosted by ENRESA, the Spanish agency responsible for the management of radioactive waste and the dismantling of nuclear power plants, and the Council of Nuclear Safety (CSN), with the support of the Association of Spanish Municipalities in Areas Surrounding Nuclear Power Plants (AMAC). The workshop took place at L'Hospitalet de l'Infant, Catalonia, Spain, on 21-23 November 2005. At this workshop, Spanish stakeholders and delegates from 14 countries discussed current co-ordination of radioactive waste management decision making in Spain. Findings were shared from Cowam-Spain, a co-operative research project on the involvement of local stakeholders, the relationship between national and local levels of decision making, and the long-term sustainability of decisions regarding the siting of a centralized interim storage facility for high-level waste. These proceedings include the workshop presentations and discussions, as well as the rapporteurs' reflections on what was learned about policy making and participative decision making. (author)

Transient Co-Expression of Post-Transcriptional Gene Silencing Suppressors for Increased in Planta Expression of a Recombinant Anthrax Receptor Fusion Protein

Directory of Open Access Journals (Sweden)

Kittipong Rattanaporn

2011-08-01

Full Text Available Potential epidemics of infectious diseases and the constant threat of bioterrorism demand rapid, scalable, and cost-efficient manufacturing of therapeutic proteins. Molecular farming of tobacco plants provides an alternative for the recombinant production of therapeutics. We have developed a transient production platform that uses Agrobacterium infiltration of Nicotiana benthamiana plants to express a novel anthrax receptor decoy protein (immunoadhesin, CMG2-Fc. This chimeric fusion protein, designed to protect against the deadly anthrax toxins, is composed of the von Willebrand factor A (VWA domain of human capillary morphogenesis 2 (CMG2, an effective anthrax toxin receptor, and the Fc region of human immunoglobulin G (IgG. We evaluated, in N. benthamiana intact plants and detached leaves, the expression of CMG2-Fc under the control of the constitutive CaMV 35S promoter, and the co-expression of CMG2-Fc with nine different viral suppressors of post-transcriptional gene silencing (PTGS: p1, p10, p19, p21, p24, p25, p38, 2b, and HCPro. Overall, transient CMG2-Fc expression was higher on intact plants than detached leaves. Maximum expression was observed with p1 co-expression at 3.5 days post-infiltration (DPI, with a level of 0.56 g CMG2-Fc per kg of leaf fresh weight and 1.5% of the total soluble protein, a ten-fold increase in expression when compared to absence of suppression. Co-expression with the p25 PTGS suppressor also significantly increased the CMG2-Fc expression level after just 3.5 DPI.

Transient co-expression of post-transcriptional gene silencing suppressors for increased in planta expression of a recombinant anthrax receptor fusion protein.

Science.gov (United States)

Arzola, Lucas; Chen, Junxing; Rattanaporn, Kittipong; Maclean, James M; McDonald, Karen A

2011-01-01

Potential epidemics of infectious diseases and the constant threat of bioterrorism demand rapid, scalable, and cost-efficient manufacturing of therapeutic proteins. Molecular farming of tobacco plants provides an alternative for the recombinant production of therapeutics. We have developed a transient production platform that uses Agrobacterium infiltration of Nicotiana benthamiana plants to express a novel anthrax receptor decoy protein (immunoadhesin), CMG2-Fc. This chimeric fusion protein, designed to protect against the deadly anthrax toxins, is composed of the von Willebrand factor A (VWA) domain of human capillary morphogenesis 2 (CMG2), an effective anthrax toxin receptor, and the Fc region of human immunoglobulin G (IgG). We evaluated, in N. benthamiana intact plants and detached leaves, the expression of CMG2-Fc under the control of the constitutive CaMV 35S promoter, and the co-expression of CMG2-Fc with nine different viral suppressors of post-transcriptional gene silencing (PTGS): p1, p10, p19, p21, p24, p25, p38, 2b, and HCPro. Overall, transient CMG2-Fc expression was higher on intact plants than detached leaves. Maximum expression was observed with p1 co-expression at 3.5 days post-infiltration (DPI), with a level of 0.56 g CMG2-Fc per kg of leaf fresh weight and 1.5% of the total soluble protein, a ten-fold increase in expression when compared to absence of suppression. Co-expression with the p25 PTGS suppressor also significantly increased the CMG2-Fc expression level after just 3.5 DPI.

Nuclear material accounting and control: Co-ordinating assistance to newly independent States

International Nuclear Information System (INIS)

Thorstensen, S.

1995-01-01

This article outlines work under way among the IAEA, its Member States, and the Newly Independent States (NIS) relating to the establishment and development in the NIS of State Systems of Accounting and Control (SSACs) of nuclear material. It describes IAEA activities in the NIS, including fact-finding missions at technical visits, the successful attempts to find donor States providing voluntary funding and expertise, and the co-ordination of technical support between the IAEA and the donor States. 3 tabs

Co-ordinate expression of activin A and its type I receptor mRNAs during phorbol ester-induced differentiation of human K562 erythroleukemia cells.

Science.gov (United States)

Hildén, K; Tuuri, T; Erämaa, M; Ritvos, O

1999-07-20

Activins were originally isolated based on their ability to stimulate follicle-stimulating hormone secretion but later they have been shown to regulate a number of different cellular functions such as nerve cell survival, mesoderm induction during early embryogenesis as well as hematopoiesis. We studied the regulation of activin A, a homodimer of betaA-subunits, mRNA and protein in K562 erythroleukemia cells, which are known to be induced toward the erythroid lineage in response to activin or TGF-beta or toward the megakaryocytic lineage by the phorbol ester protein kinase C activator 12-O-tetradecanoylphorbol-13-acetate (TPA). Here we show by Northern blot analysis as well as by Western and ligand blotting that TPA strongly promotes activin betaA-subunit mRNA and activin A protein expression in K562 cells in time- and concentration dependent manner. In contrast, neither activin A nor TGF-beta induced betaA-subunit mRNA expression during erythroid differentiation in K562 cells. Interestingly, whereas activin type II receptors are not regulated during K562 cell differentiation (Hilden et al. (1994) Blood 83, 2163-2170), we now show that the activin type I and IB receptor mRNAs are clearly induced by TPA but not by activin or TGF-beta. We also show that the inducing effect of TPA on expression of activin betaA-subunit mRNA is potentiated by the protein kinase A activator 8-bromo-cAMP. We conclude that activin A and its type I receptors appear to be co-ordinately up-regulated during megakaryocytic differentiation of K562 cells.

Report of the first research co-ordination meeting on the co-ordinated research programme: Rapid instrumental and separation methods for monitoring radionuclides in food and environmental samples, Central Laboratory for Radiological Protection, Warsaw, Poland 4-8 September 1989

International Nuclear Information System (INIS)

1989-09-01

Concern about the release of radionuclides to the environment, especially to the foodchain, has been heightened by recent nuclear incidents. The assessment of any release of radioactivity demands rapid, reliable and practical techniques. In the intermediate and late post-accident period, where the interest is in food control rather then evacuation and sheltering, rapid methods would be useful for screening purposes as well as providing timely information and easing sample workload minimizing sample overloads. In the first research co-ordination meeting on the co-ordinated research program ''Rapid.... samples'', the specifications for the time required for sample preparation, separation, and analysis and the accuracy desired were outlined. Considerable attention was given to the need to develop rapid method for sample preparation and dissolution. Emphasis was placed on achieving the development of rapid methods with the minimum sacrifice in reliability, practicality and economy

Clustering approaches to identifying gene expression patterns from DNA microarray data.

Science.gov (United States)

Do, Jin Hwan; Choi, Dong-Kug

2008-04-30

The analysis of microarray data is essential for large amounts of gene expression data. In this review we focus on clustering techniques. The biological rationale for this approach is the fact that many co-expressed genes are co-regulated, and identifying co-expressed genes could aid in functional annotation of novel genes, de novo identification of transcription factor binding sites and elucidation of complex biological pathways. Co-expressed genes are usually identified in microarray experiments by clustering techniques. There are many such methods, and the results obtained even for the same datasets may vary considerably depending on the algorithms and metrics for dissimilarity measures used, as well as on user-selectable parameters such as desired number of clusters and initial values. Therefore, biologists who want to interpret microarray data should be aware of the weakness and strengths of the clustering methods used. In this review, we survey the basic principles of clustering of DNA microarray data from crisp clustering algorithms such as hierarchical clustering, K-means and self-organizing maps, to complex clustering algorithms like fuzzy clustering.

Gene expression patterns combined with network analysis identify hub genes associated with bladder cancer.

Science.gov (United States)

Bi, Dongbin; Ning, Hao; Liu, Shuai; Que, Xinxiang; Ding, Kejia

2015-06-01

To explore molecular mechanisms of bladder cancer (BC), network strategy was used to find biomarkers for early detection and diagnosis. The differentially expressed genes (DEGs) between bladder carcinoma patients and normal subjects were screened using empirical Bayes method of the linear models for microarray data package. Co-expression networks were constructed by differentially co-expressed genes and links. Regulatory impact factors (RIF) metric was used to identify critical transcription factors (TFs). The protein-protein interaction (PPI) networks were constructed by the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and clusters were obtained through molecular complex detection (MCODE) algorithm. Centralities analyses for complex networks were performed based on degree, stress and betweenness. Enrichment analyses were performed based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Co-expression networks and TFs (based on expression data of global DEGs and DEGs in different stages and grades) were identified. Hub genes of complex networks, such as UBE2C, ACTA2, FABP4, CKS2, FN1 and TOP2A, were also obtained according to analysis of degree. In gene enrichment analyses of global DEGs, cell adhesion, proteinaceous extracellular matrix and extracellular matrix structural constituent were top three GO terms. ECM-receptor interaction, focal adhesion, and cell cycle were significant pathways. Our results provide some potential underlying biomarkers of BC. However, further validation is required and deep studies are needed to elucidate the pathogenesis of BC. Copyright © 2015 Elsevier Ltd. All rights reserved.

Co-ordinate variations in methylmalonyl-CoA mutase and methionine synthase, and the cobalamin cofactors in human glioma cells during nitrous oxide exposure and the subsequent recovery phase.

Science.gov (United States)

Riedel, B; Fiskerstrand, T; Refsum, H; Ueland, P M

1999-07-01

We investigated the co-ordinate variations of the two cobalamin (Cbl)-dependent enzymes, methionine synthase (MS) and methylmalonyl-CoA mutase (MCM), and measured the levels of their respective cofactors, methylcobalamin (CH3Cbl) and adenosylcobalamin (AdoCbl) in cultured human glioma cells during nitrous oxide exposure and during a subsequent recovery period of culture in a nitrous oxide-free atmosphere (air). In agreement with published data, MS as the primary target of nitrous oxide was inactivated rapidly (initial rate of 0.06 h(-1)), followed by reduction of CH3Cbl (to ordinate distribution of Cbl cofactors during depletion and repletion.

Gene expression profiling reveals multiple toxicity endpoints induced by hepatotoxicants

Energy Technology Data Exchange (ETDEWEB)

Huang Qihong; Jin Xidong; Gaillard, Elias T.; Knight, Brian L.; Pack, Franklin D.; Stoltz, James H.; Jayadev, Supriya; Blanchard, Kerry T

2004-05-18

Microarray technology continues to gain increased acceptance in the drug development process, particularly at the stage of toxicology and safety assessment. In the current study, microarrays were used to investigate gene expression changes associated with hepatotoxicity, the most commonly reported clinical liability with pharmaceutical agents. Acetaminophen, methotrexate, methapyrilene, furan and phenytoin were used as benchmark compounds capable of inducing specific but different types of hepatotoxicity. The goal of the work was to define gene expression profiles capable of distinguishing the different subtypes of hepatotoxicity. Sprague-Dawley rats were orally dosed with acetaminophen (single dose, 4500 mg/kg for 6, 24 and 72 h), methotrexate (1 mg/kg per day for 1, 7 and 14 days), methapyrilene (100 mg/kg per day for 3 and 7 days), furan (40 mg/kg per day for 1, 3, 7 and 14 days) or phenytoin (300 mg/kg per day for 14 days). Hepatic gene expression was assessed using toxicology-specific gene arrays containing 684 target genes or expressed sequence tags (ESTs). Principal component analysis (PCA) of gene expression data was able to provide a clear distinction of each compound, suggesting that gene expression data can be used to discern different hepatotoxic agents and toxicity endpoints. Gene expression data were applied to the multiplicity-adjusted permutation test and significantly changed genes were categorized and correlated to hepatotoxic endpoints. Repression of enzymes involved in lipid oxidation (acyl-CoA dehydrogenase, medium chain, enoyl CoA hydratase, very long-chain acyl-CoA synthetase) were associated with microvesicular lipidosis. Likewise, subsets of genes associated with hepatotocellular necrosis, inflammation, hepatitis, bile duct hyperplasia and fibrosis have been identified. The current study illustrates that expression profiling can be used to: (1) distinguish different hepatotoxic endpoints; (2) predict the development of toxic endpoints; and

Report of the second research co-ordination meeting on the co-ordinated research programme: rapid instrumental and separation methods for monitoring radionuclides in food and environmental samples

International Nuclear Information System (INIS)

1992-10-01

The purpose of this Second Research Co-ordinated Meeting (12-16 August 1991) on Rapid Instrumental and Separation Methods for Monitoring Radionuclides in Food and Environmental Samples is to discuss the progress of the programmes since the First Research Co-ordination Meeting, discuss how to validate the methodologies developed (e.g. reference samples, intercomparisons), and outline a schedule for CRP completion by the end of 1992. Radioactive contamination of the environment after a nuclear accident, such as had occurred at Chernobyl, is of serious concern to government officials and members of the general public. In 1990/1991 the Agency was asked to organize the International Chernobyl Project to assess the situation in the USSR. A network of laboratories was organized to carry out the environmental assessment needed for this project. The following recommendations are based on the experience gained by many of the laboratories involved in this project. 1. Maintain a network of analytical laboratories with special skills and experience to provide assessments of radionuclide contamination in the environment in case of a radiological emergency. 2. Methodologies for assessment of contamination in the environment should take into consideration potential trajectories, radioecology, and food chain parameters. 3. Focus on areas of representative sample collection, is situ instrumental and chemical analysis, as well as advanced streamlined laboratory analyses which will facilitate the timeline of an assessment. 4. Conduct intercomparison and testing of technologies, employing standard reference materials and procedures, and field measurements at significantly contaminated area. 5. Conduct training of Member State laboratory personnel through fellowships, special courses, and workshops. 5 refs

Report of the first research co-ordination meeting on the co-ordinated research programme: Development and selection of analytical techniques for measuring accidentally released radionuclides in environment

International Nuclear Information System (INIS)

2001-01-01

The participants at the second Research Co-ordination Meeting (Vienna, 12-16 August 1991) of the CRP on 'Rapid Instrumental and Separation Methods for Monitoring Radionuclides in Food and Environmental Samples', recommended that a new CRP be established. The current CRP on 'Development and Selection of Analytical Techniques and Procedures for Measuring Accidentally Released Radionuclides in Environment' was established based on this recommendation. The objectives of this CRP are to conduct research and development on applicable methodologies for response to accidental releases, and to improve and maintain the capabilities of the network of laboratories and provide training of individuals within member states. Thus, the CRP serves as a vehicle to maintain contact within the network of laboratories, while developing and transferring analytical techniques and procedures for measuring accidentally released radioactivity. The purpose of the Research Co-ordination Meeting is to discuss the proposed research programs, the status to date and the work planned for the duration of the CRP. The meeting also provides the opportunity for the CRP participants to exchange ideas and possibly develop collaborations in their research. The members of the CRP also need to discuss issues related to the previous CRP on Rapid methods. These include: the preparation of the final report of the previous CRP, the preparation of an addendum to TRS-295 and the ultimate revision or updating of TRS-295. Finally, it is intended that the members of the CRP should discuss the mandate and scope of work of the network of analytical laboratories and the steps needed to firmly establish this network

Co-ordinated research programme on operator support systems in nuclear power plants. Working material

International Nuclear Information System (INIS)

1993-01-01

In September 1991 the Co-ordinated Research Programme (CRP) on ''Operator Support Systems (OSSs) in Nuclear Power Plants'' was approved in the framework of the Project ''Man-Machine Interface Studies''. The main objective of the programme is to provide guidance and technology transfer in the development and implementation of OSSs. This includes the experience with man-machine interfaces and closely related issues such as control and instrumentation, the use of computers, and operator qualification. The first Co-ordinated Research Meeting held in Vienna, 13-16 October 1992, prepared a summary report which defined the tasks and the responsibilities of the CRP participants. A time schedule and future actions were also agreed upon at this meeting. The second meeting was held in Budapest, Hungary, from 5 to 8 October 1993 and was sponsored by the KFKI Atomic Energy Research Institute. The meeting reviewed the progress of the tasks defined by the first meeting, considered reports on national activities in the subject area, and agreed on time schedule and future actions. The present volume contains: (1) report prepared by the CRP meeting, (2) reports presented by the national delegates, and (3) CRP background and working plan. Refs, figs and tabs

In silico identification of miRNAs and their target genes and analysis of gene co-expression network in saffron (Crocus sativus L.) stigma

Science.gov (United States)

Zinati, Zahra; Shamloo-Dashtpagerdi, Roohollah; Behpouri, Ali

2016-01-01

As an aromatic and colorful plant of substantive taste, saffron (Crocus sativus L.) owes such properties of matter to growing class of the secondary metabolites derived from the carotenoids, apocarotenoids. Regarding the critical role of microRNAs in secondary metabolic synthesis and the limited number of identified miRNAs in C. sativus, on the other hand, one may see the point how the characterization of miRNAs along with the corresponding target genes in C. sativus might expand our perspectives on the roles of miRNAs in carotenoid/apocarotenoid biosynthetic pathway. A computational analysis was used to identify miRNAs and their targets using EST (Expressed Sequence Tag) library from mature saffron stigmas. Then, a gene co- expression network was constructed to identify genes which are potentially involved in carotenoid/apocarotenoid biosynthetic pathways. EST analysis led to the identification of two putative miRNAs (miR414 and miR837-5p) along with the corresponding stem- looped precursors. To our knowledge, this is the first report on miR414 and miR837-5p in C. sativus. Co-expression network analysis indicated that miR414 and miR837-5p may play roles in C. sativus metabolic pathways and led to identification of candidate genes including six transcription factors and one protein kinase probably involved in carotenoid/apocarotenoid biosynthetic pathway. Presence of transcription factors, miRNAs and protein kinase in the network indicated multiple layers of regulation in saffron stigma. The candidate genes from this study may help unraveling regulatory networks underlying the carotenoid/apocarotenoid biosynthesis in saffron and designing metabolic engineering for enhanced secondary metabolites. PMID:28261627

Bioremediation of trace cobalt from simulated spent decontamination solutions of nuclear power reactors using E. coli expressing NiCoT genes

International Nuclear Information System (INIS)

Raghu, G.; Maruthi Mohan, P.; Balaji, V.; Venkateswaran, G.; Rodrigue, A.; Lyon 1 Univ., 69

2008-01-01

Removal of radioactive cobalt at trace levels (∼nM) in the presence of large excess (10 6 -fold) of corrosion product ions of complexed Fe, Cr, and Ni in spent chemical decontamination formulations (simulated effluent) of nuclear reactors is currently done by using synthetic organic ion exchangers. A large volume of solid waste is generated due to the nonspecific nature of ion sorption. Our earlier work using various fungi and bacteria, with the aim of nuclear waste volume reduction, realized up to 30% of Co removal with specific capacities calculated up to 1 μg/g in 6-24 h. In the present study using engineered Escherichia coli expressing NiCoT genes from Rhodopseudomonas palustris CGA009 (RP) and Novosphingobium aromaticivorans F-199 (NA), we report a significant increase in the specific capacity for Co removal (12 μg/g) in 1-h exposure to simulated effluent. About 85% of Co removal was achieved in a two-cycle treatment with the cloned bacteria. Expression of NiCoT genes in the E. coli knockout mutant of NiCoT efflux gene (rcnA) was more efficient as compared to expression in wild-type E. coli MC4100, JM109 and BL21 (DE3) hosts. The viability of the E. coli strains in the formulation as well as at different doses of gamma rays exposure and the effect of gamma dose on their cobalt removal capacity are determined. The potential application scheme of the above process of bioremediation of cobalt from nuclear power reactor chemical decontamination effluents is discussed. (orig.)

Treatment technologies for low and intermediate level waste from nuclear applications. Final report of a co-ordinated research programme 1991-1996

International Nuclear Information System (INIS)

1997-02-01

Low and intermediate level radioactive waste is generated from the use of radioactive materials in industrial applications, research and medicine. The waste management programmes and activities in many developing Member States have been reviewed through a Waste Management Advisory Programme (WAMAP) implemented by the IAEA in 1987-1995. One of the WAMAP objectives was to assist in practical development and implementation of safe and efficient waste treatment methods. In this context the IAEA has initiated a co-ordinated research programme on treatment technologies for institutional wastes covering the most important recurring problems in developing Member States. The programme was intended to cover the research and development required for reliable waste treatment operations, including the likely variations in institutional waste inputs using simple low cost processes. This co-ordinated research programme was initiated in 1991 and brought together 14 participants from 13 countries. The results of the studies were discussed at three research co-ordination meetings. This report summarizes the salient features and results obtained during five year investigations and provides recommendations for future work in this area. Refs, figs, tabs

Treatment technologies for low and intermediate level waste from nuclear applications. Final report of a co-ordinated research programme 1991-1996

Energy Technology Data Exchange (ETDEWEB)

NONE

1997-02-01

Low and intermediate level radioactive waste is generated from the use of radioactive materials in industrial applications, research and medicine. The waste management programmes and activities in many developing Member States have been reviewed through a Waste Management Advisory Programme (WAMAP) implemented by the IAEA in 1987-1995. One of the WAMAP objectives was to assist in practical development and implementation of safe and efficient waste treatment methods. In this context the IAEA has initiated a co-ordinated research programme on treatment technologies for institutional wastes covering the most important recurring problems in developing Member States. The programme was intended to cover the research and development required for reliable waste treatment operations, including the likely variations in institutional waste inputs using simple low cost processes. This co-ordinated research programme was initiated in 1991 and brought together 14 participants from 13 countries. The results of the studies were discussed at three research co-ordination meetings. This report summarizes the salient features and results obtained during five year investigations and provides recommendations for future work in this area. Refs, figs, tabs.

Report on the consultants' meeting on co-ordination of the nuclear reaction data centres. (Technical aspects)

International Nuclear Information System (INIS)

Schwerer, O.; Lammer, M.; Pronyaev, V.G.

1999-08-01

This report summarizes the 1999 Co-ordination Meeting on Technical Aspects of the Co-operation of the Nuclear Reaction Data Centres, hold at the IAEA Headquarters in Vienna, Austria, 18 to 20 May 1999. The meeting was attended by scientists from 11 Nuclear Data Centres from 7 Member States and 2 International Organizations. The present document contains a meeting summary, the conclusions and actions, and progress reports of the Participating Data Centres. (author)

Differential effects of Pseudomonas mendocina and Glomus intraradices on lettuce plants physiological response and aquaporin PIP2 gene expression under elevated atmospheric CO2 and drought.

Science.gov (United States)

Alguacil, Maria Del Mar; Kohler, Josef; Caravaca, Fuensanta; Roldán, Antonio

2009-11-01

Arbuscular mycorrhizal (AM) symbiosis and plant-growth-promoting rhizobacterium (PGPR) can alleviate the effects of water stress in plants, but it is unknown whether these benefits can be maintained at elevated CO2. Therefore, we carried out a study where seedlings of Lactuca sativa were inoculated with the AM fungus (AMF) Glomus intraradices N.C. Schenk & G.S. Sm. or the PGPR Pseudomonas mendocina Palleroni and subjected to two levels of watering and two levels of atmospheric CO2 to ascertain their effects on plant physiological parameters and gene expression of one PIP aquaporin in roots. The inoculation with PGPR produced the greatest growth in lettuce plants under all assayed treatments as well as the highest foliar potassium concentration and leaf relative water content under elevated [CO2] and drought. However, under such conditions, the PIP2 gene expression remained almost unchanged. G. intraradices increased significantly the AMF colonization, foliar phosphorus concentration and leaf relative water content in plants grown under drought and elevated [CO2]. Under drought and elevated [CO2], the plants inoculated with G. intraradices showed enhanced expression of the PIP2 gene as compared to P. mendocina or control plants. Our results suggest that both microbial inoculation treatments could help to alleviate drought at elevated [CO2]. However, the PIP2 gene expression was increased only by the AMF but not by the PGPR under these conditions.

Integration of liver gene co-expression networks and eGWAs analyses highlighted candidate regulators implicated in lipid metabolism in pigs.

Science.gov (United States)

Ballester, Maria; Ramayo-Caldas, Yuliaxis; Revilla, Manuel; Corominas, Jordi; Castelló, Anna; Estellé, Jordi; Fernández, Ana I; Folch, Josep M

2017-04-19

In the present study, liver co-expression networks and expression Genome Wide Association Study (eGWAS) were performed to identify DNA variants and molecular pathways implicated in the functional regulatory mechanisms of meat quality traits in pigs. With this purpose, the liver mRNA expression of 44 candidates genes related with lipid metabolism was analysed in 111 Iberian x Landrace backcross animals. The eGWAS identified 92 eSNPs located in seven chromosomal regions and associated with eight genes: CROT, CYP2U1, DGAT1, EGF, FABP1, FABP5, PLA2G12A, and PPARA. Remarkably, cis-eSNPs associated with FABP1 gene expression which may be determining the C18:2(n-6)/C18:3(n-3) ratio in backfat through the multiple interaction of DNA variants and genes were identified. Furthermore, a hotspot on SSC8 associated with the gene expression of eight genes was identified and the TBCK gene was pointed out as candidate gene regulating it. Our results also suggested that the PI3K-Akt-mTOR pathway plays an important role in the control of the analysed genes highlighting nuclear receptors as the NR3C1 or PPARA. Finally, sex-dimorphism associated with hepatic lipid metabolism was identified with over-representation of female-biased genes. These results increase our knowledge of the genetic architecture underlying fat composition traits.

Gene expression profiling of brakeless mutant Drosophila embryos.

Science.gov (United States)

Crona, Filip; Singla, Bhumica; Mannervik, Mattias

2015-12-01

The transcriptional co-regulator Brakeless performs many important functions during Drosophila development, but few target genes have been identified. Here we use Affymetrix microarrays to identify Brakeless-regulated genes in 2-4 h old Drosophila embryos. Robust multi-array analysis (RMA) and statistical tests revealed 240 genes that changed their expression more than 1.5 fold. We find that up- and down-regulated genes fall into distinct gene ontology categories. In our associated study [2] we demonstrate that both up- and down-regulated genes can be direct Brakeless targets. Our results indicate that the co-repressor and co-activator activities of Brakeless may result in distinct biological responses. The microarray data complies with MIAME guidelines and is deposited in GEO under accession number GSE60048.

GR and ER co-activation alters the expression of differentiation genes and associates with improved ER+ breast cancer outcome

Science.gov (United States)

West, Diana C.; Pan, Deng; Tonsing-Carter, Eva Y.; Hernandez, Kyle M.; Pierce, Charles F.; Styke, Sarah C.; Bowie, Kathleen R.; Garcia, Tzintzuni I.; Kocherginsky, Masha; Conzen, Suzanne D.

2016-01-01

In estrogen receptor (ER)-negative breast cancer (BC), high tumor glucocorticoid receptor (GR) expression has been associated with a relatively poor outcome. In contrast, using a meta-analysis of several genomic datasets, here we find that tumor GR mRNA expression is associated with improved ER+ relapse-free survival (RFS) (independently of progesterone receptor (PR) expression). To understand the mechanism by which GR expression is associated with a better ER+ BC outcome, the global effect of GR-mediated transcriptional activation in ER+ BC cells was studied. Analysis of GR chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) in ER+/GR+ MCF-7 cells revealed that upon co-activation of GR and ER, GR chromatin association became enriched at proximal promoter regions. Furthermore, following ER activation, increased GR chromatin association was observed at ER, FOXO, and AP1 response elements. In addition, ER associated with GR response elements, suggesting that ER and GR interact in a complex. Co-activation of GR and ER resulted in increased expression (relative to ER activation alone) of transcripts that encode proteins promoting cellular differentiation (e.g. KDM4B, VDR) and inhibiting the Wnt-signaling pathway (IGFBP4). Finally, expression of these individual pro-differentiation genes was associated with significantly improved RFS in ER+ BC patients. Together, these data suggest that the co-expression and subsequent activity of tumor cell GR and ER contribute to the less aggressive natural history of early-stage BC by coordinating the altered expression of genes favoring differentiation. Implications The interaction between estrogen and glucocorticoid receptor activity highlights the importance of context-dependent nuclear receptor function in cancer. PMID:27141101

Glutamatergic induction of CREB phosphorylation and Fos expression in primary cultures of the suprachiasmatic hypothalamus in vitro is mediated by co-ordinate activity of NMDA and non-NMDA receptors.

Science.gov (United States)

Schurov, I L; McNulty, S; Best, J D; Sloper, P J; Hastings, M H

1999-01-01

Exposure of Syrian hamsters to light 1 h after lights-off rapidly (10 min) induced nuclear immunoreactivity (-ir) to the phospho-Ser133 form of the Ca2+/cAMP response element (CRE) binding protein (pCREB) in the retinorecipient zone of the suprachiasmatic nuclei (SCN). Light also induced nuclear Fos-ir in the same region of the SCN after 1 h. The glutamatergic N-methyl-D-aspartate (NMDA) receptor blocker MK801 attenuated the photic induction of both factors. To investigate glutamatergic regulation of pCREB and Fos further, tissue blocks and primary cultures of neonatal hamster SCN were examined by Western blotting and immunocytochemistry in vitro. On Western blots of SCN tissue, the pCREB-ir signal at 45 kDa was enhanced by glutamate or a mixture of glutamatergic agonists (NMDA, amino-methyl proprionic acid (AMPA), and Kainate (KA)), whereas total CREB did not change. Glutamate or the mixture of agonists also induced a 56 kDa band identified as Fos protein in SCN tissue. In dissociated cultures of SCN, glutamate caused a rapid (15 min) induction of nuclear pCREB-ir and Fos-ir (after 60 min) exclusively in neurones, both GABA-ir and others. Treatment with NMDA alone had no effect on pCREB-ir. AMPA alone caused a slight increase in pCREB-ir. However, kainate alone or in combination with NMDA and AMPA induced nuclear pCREB-ir equal to that induced by glutamate. The effects of glutamate on pCREB-ir and Fos-ir were blocked by antagonists of both NMDA (MK801) and AMPA/KA (NBQX) receptors. In the absence of extracellular Mg2+, MK801 blocked glutamatergic induction of Fos-ir. However, the AMPA/KA receptor antagonist was no longer effective at blocking glutamatergic induction of either Fos-ir or pCREB-ir, consistent with the model that glutamate regulates gene expression in the SCN by a co-ordinate action through both NMDA and AMPA/KA receptors. Glutamatergic induction of nuclear pCREB-ir in GABA-ir neurones was blocked by KN-62 an inhibitor of Ca2+/Calmodulin (Ca

1st IAEA research co-ordination meeting on 'plasma-material interaction data for mixed plasma facing materials in fusion reactors'. Summary report

International Nuclear Information System (INIS)

Janev, R.K.; Longhurst, G.

1998-12-01

The proceedings and conclusions of the 1st IAEA Research Co-ordination Meeting on 'Plasma-Material Interaction Data for Mixed Plasma Facing Materials in Fusion Reactors', held on December 19 and 20, 1998 at the IAEA Headquarters in Vienna, are briefly described. This report includes a summary of the presentations made by meeting participants, a review of the data availability and data needs in the areas from the scope of the Co-ordinated Research Project (CRP) on the subject of the meeting, and recommendations regarding the future work within this CRP. (author)

miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling.

Science.gov (United States)

Plaisier, Christopher L; Bare, J Christopher; Baliga, Nitin S

2011-07-01

Transcriptome profiling studies have produced staggering numbers of gene co-expression signatures for a variety of biological systems. A significant fraction of these signatures will be partially or fully explained by miRNA-mediated targeted transcript degradation. miRvestigator takes as input lists of co-expressed genes from Caenorhabditis elegans, Drosophila melanogaster, G. gallus, Homo sapiens, Mus musculus or Rattus norvegicus and identifies the specific miRNAs that are likely to bind to 3' un-translated region (UTR) sequences to mediate the observed co-regulation. The novelty of our approach is the miRvestigator hidden Markov model (HMM) algorithm which systematically computes a similarity P-value for each unique miRNA seed sequence from the miRNA database miRBase to an overrepresented sequence motif identified within the 3'-UTR of the query genes. We have made this miRNA discovery tool accessible to the community by integrating our HMM algorithm with a proven algorithm for de novo discovery of miRNA seed sequences and wrapping these algorithms into a user-friendly interface. Additionally, the miRvestigator web server also produces a list of putative miRNA binding sites within 3'-UTRs of the query transcripts to facilitate the design of validation experiments. The miRvestigator is freely available at http://mirvestigator.systemsbiology.net.

The effect of industry clockspeed on supply chain co-ordination: Classical theory to sharpen an emerging concept

NARCIS (Netherlands)

Meijboom, Bert; Voordijk, Johannes T.; Akkermans, Henk

2007-01-01

Purpose – The relevance of “industry clockspeed” to supply chain co-ordination (SCC) has recently been stressed but hardly been researched. Taking an information-processing perspective, the purpose of this paper is to examine the development of SCC theory under varying clockspeed circumstances.

Co-Expression and Co-Localization of Cartilage Glycoproteins CHI3L1 and Lubricin in Osteoarthritic Cartilage: Morphological, Immunohistochemical and Gene Expression Profiles

Directory of Open Access Journals (Sweden)

Marta Anna Szychlinska

2016-03-01

Full Text Available Osteoarthritis is the most common human arthritis characterized by degeneration of articular cartilage. Several studies reported that levels of human cartilage glycoprotein chitinase 3-like-1 (CHI3L1 are known as a potential marker for the activation of chondrocytes and the progression of Osteoarthritis (OA, whereas lubricin appears to be chondroprotective. The aim of this study was to investigate the co-expression and co-localization of CHI3L1 and lubricin in normal and osteoarthritic rat articular cartilage to correlate their modified expression to a specific grade of OA. Samples of normal and osteoarthritic rat articular cartilage were analyzed by the Kellgren–Lawrence OA severity scores, the Kraus’ modified Mankin score and the Histopathology Osteoarthritis Research Society International (OARSI system for histomorphometric evaluations, and through CHI3L1 and lubricin gene expression, immunohistochemistry and double immuno-staining analysis. The immunoexpression and the mRNA levels of lubricin increased in normal cartilage and decreased in OA cartilage (normal vs. OA, p < 0.01. By contrast, the immunoexpression and the mRNA levels of CHI3L1 increased in OA cartilage and decreased in normal cartilage (normal vs. OA, p < 0.01. Our findings are consistent with reports suggesting that these two glycoproteins are functionally associated with the development of OA and in particular with grade 2/3 of OA, suggesting that in the future they could be helpful to stage the severity and progression of the disease.

2nd (final) IAEA research co-ordination meeting on 'plasma-material interaction data for mixed plasma facing materials in fusion reactors'. Summary report

International Nuclear Information System (INIS)

Clark, R.E.H.

2001-11-01

The proceedings and conclusions of the 2nd Research Co-ordination Meeting on 'Plasma-Material Interaction Data for Mixed Plasma Facing Materials in Fusion Reactors', held on October 16 and 17, 2000 at the IAEA Headquarters in Vienna, are briefly described. This report includes a summary of the presentations made by the meeting participants and a review of the accomplishments of the Co-ordinated Research Project (CRP). In addition, short summaries from the participants are included indicating the specific research completed in support of this CRP. (author)

The production of lymphokines by primary alloreactive T-cell clones: a co-ordinate analysis of 233 clones in seven lymphokine assays.

Science.gov (United States)

Sanderson, C J; Strath, M; Warren, D J; O'Garra, A; Kirkwood, T B

1985-01-01

A total of 233 primary alloreactive T-cell clones have been tested for the production of interleukin-2 (IL-2), interleukin-3 (IL-3), immune(gamma) interferon (IFN) and granulocyte-macrophage colony-stimulating factor (CSF-2), B-cell growth factor I and II (BCGFI, BCGFII), and eosinophil differentiation factor (EDF). EDF was assayed by means of the eosinophil differentiation assay (EDA). Two principal correlations were observed: IL-3 was shown to be the major lymphokine detected in the bone marrow proliferation assay (BMPA) used to detect CSF-2, and there was a high correlation between the EDA and BCGFII. Subsequent work has suggested that this latter correlation is because a single factor is responsible for both activities. Apart from these two exceptions, and low level correlations probably due to the fact that different assays detect more than one lymphokine, there was no evidence for co-ordinate expression of lymphokines. There was a large variation in amounts of individual lymphokines produced. More clones produced multiple lymphokines than would be expected from independent control. Taken together, this pattern of regulation is consistent with the hypothesis that antigen stimulation of T cells results in the activation of all the lymphokine genes, but the amount of each produced is determined by secondary controlling mechanisms. PMID:3935571

Characterization of differentially expressed genes involved in pathways associated with gastric cancer.

Directory of Open Access Journals (Sweden)

Hao Li

Full Text Available To explore the patterns of gene expression in gastric cancer, a total of 26 paired gastric cancer and noncancerous tissues from patients were enrolled for gene expression microarray analyses. Limma methods were applied to analyze the data, and genes were considered to be significantly differentially expressed if the False Discovery Rate (FDR value was 2. Subsequently, Gene Ontology (GO categories were used to analyze the main functions of the differentially expressed genes. According to the Kyoto Encyclopedia of Genes and Genomes (KEGG database, we found pathways significantly associated with the differential genes. Gene-Act network and co-expression network were built respectively based on the relationships among the genes, proteins and compounds in the database. 2371 mRNAs and 350 lncRNAs considered as significantly differentially expressed genes were selected for the further analysis. The GO categories, pathway analyses and the Gene-Act network showed a consistent result that up-regulated genes were responsible for tumorigenesis, migration, angiogenesis and microenvironment formation, while down-regulated genes were involved in metabolism. These results of this study provide some novel findings on coding RNAs, lncRNAs, pathways and the co-expression network in gastric cancer which will be useful to guide further investigation and target therapy for this disease.

Co-expression Network Approach to Studying the Effects of Botulinum Neurotoxin-A.

Science.gov (United States)

Mukund, Kavitha; Ward, Samuel R; Lieber, Richard L; Subramaniam, Shankar

2017-10-16

Botulinum Neurotoxin A (BoNT-A) is a potent neurotoxin with several clinical applications.The goal of this study was to utilize co-expression network theory to analyze temporal transcriptional data from skeletal muscle after BoNT-A treatment. Expression data for 2000 genes (extracted using a ranking heuristic) served as the basis for this analysis. Using weighted gene co-expression network analysis (WGCNA), we identified 19 co-expressed modules, further hierarchically clustered into 5 groups. Quantifying average expression and co-expression patterns across these groups revealed temporal aspects of muscle's response to BoNT-A. Functional analysis revealed enrichment of group 1 with metabolism; group 5 with contradictory functions of atrophy and cellular recovery; and groups 2 and 3 with extracellular matrix (ECM) and non-fast fiber isoforms. Topological positioning of two highly ranked, significantly expressed genes- Dclk1 and Ostalpha within group 5 suggested possible mechanistic roles in recovery from BoNT-A induced atrophy. Phenotypic correlations of groups with titin and myosin protein content further emphasized the effect of BoNT-A on the sarcomeric contraction machinery in early phase of chemodenervation. In summary, our approach revealed a hierarchical functional response to BoNT-A induced paralysis with early metabolic and later ECM responses and identified putative biomarkers associated with chemodenervation. Additionally, our results provide an unbiased validation of the response documented in our previous workBotulinum Neurotoxin A (BoNT-A) is a potent neurotoxin with several clinical applications.The goal of this study was to utilize co-expression network theory to analyze temporal transcriptional data from skeletal muscle after BoNT-A treatment. Expression data for 2000 genes (extracted using a ranking heuristic) served as the basis for this analysis. Using weighted gene co-expression network analysis (WGCNA), we identified 19 co-expressed modules

LCGbase: A Comprehensive Database for Lineage-Based Co-regulated Genes.

Science.gov (United States)

Wang, Dapeng; Zhang, Yubin; Fan, Zhonghua; Liu, Guiming; Yu, Jun

2012-01-01

ontology (GO) annotation, promoter identification, gene expression (co-expression), and evolutionary analysis. This database not only provides a way to define lineage-specific and species-specific gene clusters but also facilitates future studies on gene co-regulation, epigenetic control of gene expression (DNA methylation and histone marks), and chromosomal structures in a context of gene clusters and species evolution. LCGbase is freely available at http://lcgbase.big.ac.cn/LCGbase.

Acyl-CoA-binding protein/diazepam-binding inhibitor gene and pseudogenes

DEFF Research Database (Denmark)

Mandrup, S; Hummel, R; Ravn, S

1992-01-01

Acyl-CoA-binding protein (ACBP) is a 10 kDa protein isolated from bovine liver by virtue of its ability to bind and induce the synthesis of medium-chain acyl-CoA esters. Surprisingly, it turned out to be identical to a protein named diazepam-binding Inhibitor (DBI) claimed to be an endogenous mod...... have molecularly cloned and characterized the ACBP/DBI gene family in rat. The rat ACBP/DBI gene family comprises one expressed gene and four processed pseudogenes of which one was shown to exist in two allelic forms. The expressed gene is organized into four exons and three introns...

Co-expression modules construction by WGCNA and identify potential prognostic markers of uveal melanoma.

Science.gov (United States)

Wan, Qi; Tang, Jing; Han, Yu; Wang, Dan

2018-01-01

Uveal melanoma is an aggressive cancer which has a high percentage recurrence and with a worse prognosis. Identify the potential prognostic markers of uveal melanoma may provide information for early detection of recurrence and treatment. RNA sequence data of uveal melanoma and patient clinic traits were obtained from The Cancer Genome Atlas (TCGA) database. Co-expression modules were built by weighted gene co -expression network analysis (WGCNA) and applied to investigate the relationship underlying modules and clinic traits. Besides, functional enrichment analysis was performed on these co-expression genes from interested modules. First, using WGCNA, identified 21 co-expression modules were constructed by the 10975 genes from the 80 human uveal melanoma samples. The number of genes in these modules ranged from 42 to 5091. Found four co -expression modules significantly correlated with three clinic traits (status, recurrence and recurrence Time). Module red, and purple positively correlated with patient's life status and recurrence Time. Module green positively correlates with recurrence. The result of functional enrichment analysis showed that the module magenta was mainly enriched genetic material assemble processes, the purple module was mainly enriched in tissue homeostasis and melanosome membrane and the module red was mainly enriched metastasis of cell, suggesting its critical role in the recurrence and development of the disease. Additionally, identified the hug gene (top connectivity with other genes) in each module. The hub gene SLC17A7, NTRK2, ABTB1 and ADPRHL1 might play a vital role in recurrence of uveal melanoma. Our findings provided the framework of co-expression gene modules of uveal melanoma and identified some prognostic markers might be detection of recurrence and treatment for uveal melanoma. Copyright © 2017 Elsevier Ltd. All rights reserved.

Production of {sup 99}Tc{sup m} radiopharmaceuticals for brain, heart and kidney imaging. Final report of a co-ordinated research programme 1991-1994

Energy Technology Data Exchange (ETDEWEB)

NONE

1995-07-01

The report contains highlights of the achievements of the IAEA Co-ordinated Research programme on Evaluation on the Use of Bulk Reagents for the Production of {sup 99}Tc{sub m} Radiopharmaceutical and Kits, the participants` summary reports (Argentina, Chile, Greece, India, Indonesia, Japan, Malaysia, Portugal, Russian Federation, Thailand, Uruguay, United States of America), recommended product protocols for five compounds and the participants` recommendations regarding continued support and further directions of co-ordinated research work. Refs, 6 figs, 8 tabs, 6 schemes.

The role of cell cycle in retinal development: cyclin-dependent kinase inhibitors co-ordinate cell-cycle inhibition, cell-fate determination and differentiation in the developing retina.

Science.gov (United States)

Bilitou, Aikaterini; Ohnuma, Shin-ichi

2010-03-01

The mature retina is formed through multi-step developmental processes, including eye field specification, optic vesicle evagination, and cell-fate determination. Co-ordination of these developmental events with cell-proliferative activity is essential to achieve formation of proper retinal structure and function. In particular, the molecular and cellular dynamics of the final cell cycle significantly influence the identity that a cell acquires, since cell fate is largely determined at the final cell cycle for the production of postmitotic cells. This review summarizes our current understanding of the cellular mechanisms that underlie the co-ordination of cell-cycle and cell-fate determination, and also describes a molecular role of cyclin-dependent kinase inhibitors (CDKIs) as co-ordinators of cell-cycle arrest, cell-fate determination and differentiation. Copyright (c) 2010 Wiley-Liss, Inc.

New ordinances

International Nuclear Information System (INIS)

Reuter, H.

1980-01-01

Based on extensive preliminary work of the responsible Federal Minister of Labour and Social Affairs, the 'Ordinance to Replace Ordinances under Article 24 of the Irading and Industrial Code' has been issued by the Federal Government on February 27, 1980. This new ordinance also contains the new versions of the Steam Boiler Ordinance, the Pressure Gas Ordinance, the Lift Ordinance, the Ordinance on Electrical Installations in Rooms with High Explosion Hazards, the Acetylene Ordinance, and the Ordinance on Combustible Liquids. Accordingly, these new ordinances all have the same date of issue. Coming into force on July 1, 1980, they will replace six ordinances for plants to be licensed. The same applies to the pertinent general administrative regulations. (orig.) [de

Changes in the gene expression of co-cultured human fibroblast cells and osteosarcoma cells: the role of microenvironment.

Science.gov (United States)

Salvatore, Viviana; Focaroli, Stefano; Teti, Gabriella; Mazzotti, Antonio; Falconi, Mirella

2015-10-06

The progression of malignant tumors does not depend exclusively on the autonomous properties of cancer cells; it is also influenced by tumor stroma reactivity and is under strict microenvironmental control. By themselves, stromal cells are not malignant, and they maintain normal tissue structure and function. However, through intercellular interactions or by paracrine secretions from cancer cells, normal stromal cells acquire abnormal phenotypes that sustain cancer cell growth and tumor progression. In their dysfunctional state, fibroblast and immune cells produce chemokines and growth factors that stimulate cancer cell growth and invasion. In our previous work, we established an in vitro model based on a monolayer co-culture system of healthy human fibroblasts (HFs) and human osteosarcoma cells (the MG-63 cell line) that simulates the microenvironment of tumor cells and healthy cells. The coexistence between MG-63 cells and HFs allowed us to identify the YKL-40 protein as the main marker for verifying the influence of tumor cells grown in contact with healthy cells. In this study, we evaluated the interactions of HFs and MG-63 cells in a transwell co-culture system over 24 h, 48 h, 72 h, and 96 h. We analyzed the contributions of these populations to the tumor microenvironment during cancer progression, as measured by multiple markers. We examined the effect of siRNA knockdown of YKL-40 by tracking the subsequent changes in gene expression within the co-culture. We validated the expression of several genes, focusing on those involved in cancer cell invasion, inflammatory responses, and angiogenesis: TNF alpha, IL-6, MMP-1, MMP-9, and VEGF. We compared the results to those from a transwell co-culture without the YKL-40 knockdown. In a pro-inflammatory environment promoted by TNF alpha and IL-6, siRNA knockdown of YKL-40 caused a down-regulation of VEGF and MMP-1 expression in HFs. These findings demonstrated that the tumor microenvironment has an influence on the

Identification of co-expression gene networks, regulatory genes and pathways for obesity based on adipose tissue RNA Sequencing in a porcine model

DEFF Research Database (Denmark)

Kogelman, Lisette; Cirera Salicio, Susanna; Zhernakova, Daria V.

2014-01-01

interactions. Identification of co-expressed and regulatory genes in RNA extracted from relevant tissues representing lean and obese individuals provides an entry point for the identification of genes and pathways of importance to the development of obesity. The pig, an omnivorous animal, is an excellent model...... (modules). Additionally, regulator genes were detected using Lemon-Tree algorithms. Results WGCNA revealed five modules which were strongly correlated with at least one obesity-related phenotype (correlations ranging from -0.54 to 0.72, P ... the association between obesity and other diseases, like osteoporosis (osteoclast differentiation, P = 1.4E-7), and immune-related complications (e.g. Natural killer cell mediated cytotoxity, P = 3.8E-5; B cell receptor signaling pathway, P = 7.2E-5). Lemon-Tree identified three potential regulator genes, using...

ESR1 Is Co-Expressed with Closely Adjacent Uncharacterised Genes Spanning a Breast Cancer Susceptibility Locus at 6q25.1

Science.gov (United States)

Dunbier, Anita K.; Anderson, Helen; Ghazoui, Zara; Lopez-Knowles, Elena; Pancholi, Sunil; Ribas, Ricardo; Drury, Suzanne; Sidhu, Kally; Leary, Alexandra; Martin, Lesley-Ann; Dowsett, Mitch

2011-01-01

Approximately 80% of human breast carcinomas present as oestrogen receptor α-positive (ER+ve) disease, and ER status is a critical factor in treatment decision-making. Recently, single nucleotide polymorphisms (SNPs) in the region immediately upstream of the ER gene (ESR1) on 6q25.1 have been associated with breast cancer risk. Our investigation of factors associated with the level of expression of ESR1 in ER+ve tumours has revealed unexpected associations between genes in this region and ESR1 expression that are important to consider in studies of the genetic causes of breast cancer risk. RNA from tumour biopsies taken from 104 postmenopausal women before and after 2 weeks treatment with an aromatase (oestrogen synthase) inhibitor was analyzed on Illumina 48K microarrays. Multiple-testing corrected Spearman correlation revealed that three previously uncharacterized open reading frames (ORFs) located immediately upstream of ESR1, C6ORF96, C6ORF97, and C6ORF211 were highly correlated with ESR1 (Rs = 0.67, 0.64, and 0.55 respectively, FDRaccount for the correlations. The correlations were maintained in cultured cells. An ERα antagonist did not affect the ORFs' expression or their correlation with ESR1, suggesting their transcriptional co-activation is not directly mediated by ERα. siRNA inhibition of C6ORF211 suppressed proliferation in MCF7 cells, and C6ORF211 positively correlated with a proliferation metagene in tumours. In contrast, C6ORF97 expression correlated negatively with the metagene and predicted for improved disease-free survival in a tamoxifen-treated published dataset, independently of ESR1. Our observations suggest that some of the biological effects previously attributed to ER could be mediated and/or modified by these co-expressed genes. The co-expression and function of these genes may be important influences on the recently identified relationship between SNPs in this region and breast cancer risk. PMID:21552322

Regulation of gene expression is associated with tolerance of the Arctic copepod Calanus glacialis to CO2-acidified sea water.

Science.gov (United States)

Bailey, Allison; De Wit, Pierre; Thor, Peter; Browman, Howard I; Bjelland, Reidun; Shema, Steven; Fields, David M; Runge, Jeffrey A; Thompson, Cameron; Hop, Haakon

2017-09-01

Ocean acidification is the increase in seawater p CO 2 due to the uptake of atmospheric anthropogenic CO 2 , with the largest changes predicted to occur in the Arctic seas. For some marine organisms, this change in p CO 2 , and associated decrease in pH, represents a climate change-related stressor. In this study, we investigated the gene expression patterns of nauplii of the Arctic copepod Calanus glacialis cultured at low pH levels. We have previously shown that organismal-level performance (development, growth, respiration) of C. glacialis nauplii is unaffected by low pH. Here, we investigated the molecular-level response to lowered pH in order to elucidate the physiological processes involved in this tolerance. Nauplii from wild-caught C. glacialis were cultured at four pH levels (8.05, 7.9, 7.7, 7.5). At stage N6, mRNA was extracted and sequenced using RNA-seq. The physiological functionality of the proteins identified was categorized using Gene Ontology and KEGG pathways. We found that the expression of 151 contigs varied significantly with pH on a continuous scale (93% downregulated with decreasing pH). Gene set enrichment analysis revealed that, of the processes downregulated, many were components of the universal cellular stress response, including DNA repair, redox regulation, protein folding, and proteolysis. Sodium:proton antiporters were among the processes significantly upregulated, indicating that these ion pumps were involved in maintaining cellular pH homeostasis. C. glacialis significantly alters its gene expression at low pH, although they maintain normal larval development. Understanding what confers tolerance to some species will support our ability to predict the effects of future ocean acidification on marine organisms.

Evolution, functional differentiation, and co-expression of the RLK gene family revealed in Jilin ginseng, Panax ginseng C.A. Meyer.

Science.gov (United States)

Lin, Yanping; Wang, Kangyu; Li, Xiangyu; Sun, Chunyu; Yin, Rui; Wang, Yanfang; Wang, Yi; Zhang, Meiping

2018-02-21

Most genes in a genome exist in the form of a gene family; therefore, it is necessary to have knowledge of how a gene family functions to comprehensively understand organismal biology. The receptor-like kinase (RLK)-encoding gene family is one of the most important gene families in plants. It plays important roles in biotic and abiotic stress tolerances, and growth and development. However, little is known about the functional differentiation and relationships among the gene members within a gene family in plants. This study has isolated 563 RLK genes (designated as PgRLK genes) expressed in Jilin ginseng (Panax ginseng C.A. Meyer), investigated their evolution, and deciphered their functional diversification and relationships. The PgRLK gene family is highly diverged and formed into eight types. The LRR type is the earliest and most prevalent, while only the Lec type originated after P. ginseng evolved. Furthermore, although the members of the PgRLK gene family all encode receptor-like protein kinases and share conservative domains, they are functionally very diverse, participating in numerous biological processes. The expressions of different members of the PgRLK gene family are extremely variable within a tissue, at a developmental stage and in the same cultivar, but most of the genes tend to express correlatively, forming a co-expression network. These results not only provide a deeper and comprehensive understanding of the evolution, functional differentiation and correlation of a gene family in plants, but also an RLK genic resource useful for enhanced ginseng genetic improvement.

Emiliania huxleyi increases calcification but not expression of calcification-related genes in long-term exposure to elevated temperature and pCO2.

Science.gov (United States)

Benner, Ina; Diner, Rachel E; Lefebvre, Stephane C; Li, Dian; Komada, Tomoko; Carpenter, Edward J; Stillman, Jonathon H

2013-01-01

Increased atmospheric pCO2 is expected to render future oceans warmer and more acidic than they are at present. Calcifying organisms such as coccolithophores that fix and export carbon into the deep sea provide feedbacks to increasing atmospheric pCO2. Acclimation experiments suggest negative effects of warming and acidification on coccolithophore calcification, but the ability of these organisms to adapt to future environmental conditions is not well understood. Here, we tested the combined effect of pCO2 and temperature on the coccolithophore Emiliania huxleyi over more than 700 generations. Cells increased inorganic carbon content and calcification rate under warm and acidified conditions compared with ambient conditions, whereas organic carbon content and primary production did not show any change. In contrast to findings from short-term experiments, our results suggest that long-term acclimation or adaptation could change, or even reverse, negative calcification responses in E. huxleyi and its feedback to the global carbon cycle. Genome-wide profiles of gene expression using RNA-seq revealed that genes thought to be essential for calcification are not those that are most strongly differentially expressed under long-term exposure to future ocean conditions. Rather, differentially expressed genes observed here represent new targets to study responses to ocean acidification and warming.

Co-expression of interleukin 12 enhances antitumor effects of a novel chimeric promoter-mediated suicide gene therapy in an immunocompetent mouse model

International Nuclear Information System (INIS)

Xu, Yu; Liu, Zhengchun; Kong, Haiyan; Sun, Wenjie; Liao, Zhengkai; Zhou, Fuxiang; Xie, Conghua

2011-01-01

Highlights: → A novel chimeric promoter consisting of CArG element and hTERT promoter was developed. → The promoter was characterized with radiation-inducibility and tumor-specificity. → Suicide gene system driven by the promoter showed remarkable cytotoxicity in vitro. → Co-expression of IL12 enhanced the promoter mediated suicide gene therapy in vivo. -- Abstract: The human telomerase reverse transcriptase (hTERT) promoter has been widely used in target gene therapy of cancer. However, low transcriptional activity limited its clinical application. Here, we designed a novel dual radiation-inducible and tumor-specific promoter system consisting of CArG elements and the hTERT promoter, resulting in increased expression of reporter genes after gamma-irradiation. Therapeutic and side effects of adenovirus-mediated horseradish peroxidase (HRP)/indole-3-acetic (IAA) system downstream of the chimeric promoter were evaluated in mice bearing Lewis lung carcinoma, combining with or without adenovirus-mediated interleukin 12 (IL12) gene driven by the cytomegalovirus promoter. The combination treatment showed more effective suppression of tumor growth than those with single agent alone, being associated with pronounced intratumoral T-lymphocyte infiltration and minor side effects. Our results suggest that the combination treatment with HRP/IAA system driven by the novel chimeric promoter and the co-expression of IL12 might be an effective and safe target gene therapy strategy of cancer.

Co-expression of interleukin 12 enhances antitumor effects of a novel chimeric promoter-mediated suicide gene therapy in an immunocompetent mouse model

Energy Technology Data Exchange (ETDEWEB)

Xu, Yu, E-mail: xuyu1001@gmail.com [Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan 430071 (China); Hubei Key Laboratory of Tumor Biological Behaviors and Hubei Cancer Clinical Study Center, 169 Donghu Road, Wuhan 430071 (China); Liu, Zhengchun, E-mail: l135027@126.com [Hubei Key Laboratory of Tumor Biological Behaviors and Hubei Cancer Clinical Study Center, 169 Donghu Road, Wuhan 430071 (China); Kong, Haiyan, E-mail: suppleant@163.com [Hubei Key Laboratory of Tumor Biological Behaviors and Hubei Cancer Clinical Study Center, 169 Donghu Road, Wuhan 430071 (China); Sun, Wenjie, E-mail: wendy11240325@163.com [Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan 430071 (China); Hubei Key Laboratory of Tumor Biological Behaviors and Hubei Cancer Clinical Study Center, 169 Donghu Road, Wuhan 430071 (China); Liao, Zhengkai, E-mail: fastbeta@gmail.com [Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan 430071 (China); Hubei Key Laboratory of Tumor Biological Behaviors and Hubei Cancer Clinical Study Center, 169 Donghu Road, Wuhan 430071 (China); Zhou, Fuxiang, E-mail: happyzhoufx@sina.com [Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan 430071 (China); Hubei Key Laboratory of Tumor Biological Behaviors and Hubei Cancer Clinical Study Center, 169 Donghu Road, Wuhan 430071 (China); Xie, Conghua, E-mail: chxie_65@hotmail.com [Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan 430071 (China); Hubei Key Laboratory of Tumor Biological Behaviors and Hubei Cancer Clinical Study Center, 169 Donghu Road, Wuhan 430071 (China); and others

2011-09-09

Highlights: {yields} A novel chimeric promoter consisting of CArG element and hTERT promoter was developed. {yields} The promoter was characterized with radiation-inducibility and tumor-specificity. {yields} Suicide gene system driven by the promoter showed remarkable cytotoxicity in vitro. {yields} Co-expression of IL12 enhanced the promoter mediated suicide gene therapy in vivo. -- Abstract: The human telomerase reverse transcriptase (hTERT) promoter has been widely used in target gene therapy of cancer. However, low transcriptional activity limited its clinical application. Here, we designed a novel dual radiation-inducible and tumor-specific promoter system consisting of CArG elements and the hTERT promoter, resulting in increased expression of reporter genes after gamma-irradiation. Therapeutic and side effects of adenovirus-mediated horseradish peroxidase (HRP)/indole-3-acetic (IAA) system downstream of the chimeric promoter were evaluated in mice bearing Lewis lung carcinoma, combining with or without adenovirus-mediated interleukin 12 (IL12) gene driven by the cytomegalovirus promoter. The combination treatment showed more effective suppression of tumor growth than those with single agent alone, being associated with pronounced intratumoral T-lymphocyte infiltration and minor side effects. Our results suggest that the combination treatment with HRP/IAA system driven by the novel chimeric promoter and the co-expression of IL12 might be an effective and safe target gene therapy strategy of cancer.

Vibrational spectra and normal co-ordinate analysis of 2-aminopyridine and 2-amino picoline.

Science.gov (United States)

Jose, Sujin P; Mohan, S

2006-05-01

The Fourier transform infrared (FT-IR) and Raman (FT-R) spectra of 2-aminopyridine and 2-amino picoline were recorded and the observed frequencies were assigned to various modes of vibration in terms of fundamentals by assuming Cs point group symmetry. A normal co-ordinate analysis was also carried out for the proper assignment of the vibrational frequencies using simple valence force field. A complete vibrational analysis is presented here for the molecules and the results are briefly discussed.

Comprehensive analysis of coding-lncRNA gene co-expression network uncovers conserved functional lncRNAs in zebrafish.

Science.gov (United States)

Chen, Wen; Zhang, Xuan; Li, Jing; Huang, Shulan; Xiang, Shuanglin; Hu, Xiang; Liu, Changning

2018-05-09

Zebrafish is a full-developed model system for studying development processes and human disease. Recent studies of deep sequencing had discovered a large number of long non-coding RNAs (lncRNAs) in zebrafish. However, only few of them had been functionally characterized. Therefore, how to take advantage of the mature zebrafish system to deeply investigate the lncRNAs' function and conservation is really intriguing. We systematically collected and analyzed a series of zebrafish RNA-seq data, then combined them with resources from known database and literatures. As a result, we obtained by far the most complete dataset of zebrafish lncRNAs, containing 13,604 lncRNA genes (21,128 transcripts) in total. Based on that, a co-expression network upon zebrafish coding and lncRNA genes was constructed and analyzed, and used to predict the Gene Ontology (GO) and the KEGG annotation of lncRNA. Meanwhile, we made a conservation analysis on zebrafish lncRNA, identifying 1828 conserved zebrafish lncRNA genes (1890 transcripts) that have their putative mammalian orthologs. We also found that zebrafish lncRNAs play important roles in regulation of the development and function of nervous system; these conserved lncRNAs present a significant sequential and functional conservation, with their mammalian counterparts. By integrative data analysis and construction of coding-lncRNA gene co-expression network, we gained the most comprehensive dataset of zebrafish lncRNAs up to present, as well as their systematic annotations and comprehensive analyses on function and conservation. Our study provides a reliable zebrafish-based platform to deeply explore lncRNA function and mechanism, as well as the lncRNA commonality between zebrafish and human.

Efficient nonlinear registration of 3D images using high order co-ordinate transfer functions.

Science.gov (United States)

Barber, D C

1999-01-01

There is an increasing interest in image registration for a variety of medical imaging applications. Image registration is achieved through the use of a co-ordinate transfer function (CTF) which maps voxels in one image to voxels in the other image, including in the general case changes in mapped voxel intensity. If images of the same subject are to be registered the co-ordinate transfer function needs to implement a spatial transformation consisting of a displacement and a rigid rotation. In order to achieve registration a common approach is to choose a suitable quality-of-registration measure and devise a method for the efficient generation of the parameters of the CTF which minimize this measure. For registration of images from different subjects more complex transforms are required. In general function minimization is too slow to allow the use of CTFs with more than a small number of parameters. However, provided the images are from the same modality and the CTF can be expanded in terms of an appropriate set of basis functions this paper will show how relatively complex CTFs can be used for registration. The use of increasingly complex CTFs to minimize the within group standard deviation of a set of normal single photon emission tomography brain images is used to demonstrate the improved registration of images from different subjects using CTFs of increasing complexity.

Research co-ordination meeting on labelling, quality control and clinical evaluation of monoclonal antibodies for scintigraphy, Kuala Lumpur, Malaysia, 9-13 September 1991

International Nuclear Information System (INIS)

1991-09-01

The Co-ordinated Research Programme (CRP) on ''Labelling, quality control and clinical evaluation of monoclonal antibodies for scintigraphy'' arose from the deliberations at an IAEA Consultants' Meeting (CM) on ''Radiolabelling techniques of monoclonal antibodies'' held in Vienna on 22-24 August 1988. The following is a brief description of the relevant recommendations arising from said meeting. A more detailed description of the proceedings may be found in the summary report issued on 8 December 1989. This report incorporates the results of the first Research Co-ordination Meeting (RCM) of subject CRP held in Kuala Lumpur, Malaysia on 9-13 September 1991. 9 refs

Acoustic signal processing for the detection of sodium boiling or sodium-water reaction in LMFRs. Final report of a co-ordinated research programme 1990-1995

International Nuclear Information System (INIS)

1997-05-01

This report is a summary of the work performed under a co-ordinated research programme entitled Acoustic Signal Processing for the Detection of Sodium Boiling or Sodium-Water Reaction in Liquid Metal Cooled Fast Reactors. The programme was organized by the IAEA and carried out from 1990 to 1995. It was the continuation of an earlier research co-ordination programme entitled Signal Processing Techniques for Sodium Boiling Noise Detection, which was carried out from 1984 to 1989. Refs, figs, tabs

Report on the IAEA consultants' meeting on the co-ordination of nuclear reaction data centres (technical aspects)

Energy Technology Data Exchange (ETDEWEB)

Schwerer, O [International Atomic Energy Agency, Nuclear Data Section, Vienna (Austria)

2001-07-01

This report summarizes the results of the IAEA Consultants' Meeting on the Co-ordination of Nuclear Reaction Data Centres (Technical Aspects), held at the IAEA Headquarters, Vienna, Austria, 28 to 30 May 2001. The meeting was attended by 16 participants from 10 co-operating data centres from six Member States and two International Organizations. The report contains a meeting summary, the conclusions and actions, progress and status reports of the participating data centres and working papers considered at the meeting. (author)

Inferring the transcriptional landscape of bovine skeletal muscle by integrating co-expression networks.

Directory of Open Access Journals (Sweden)

Nicholas J Hudson

Full Text Available BACKGROUND: Despite modern technologies and novel computational approaches, decoding causal transcriptional regulation remains challenging. This is particularly true for less well studied organisms and when only gene expression data is available. In muscle a small number of well characterised transcription factors are proposed to regulate development. Therefore, muscle appears to be a tractable system for proposing new computational approaches. METHODOLOGY/PRINCIPAL FINDINGS: Here we report a simple algorithm that asks "which transcriptional regulator has the highest average absolute co-expression correlation to the genes in a co-expression module?" It correctly infers a number of known causal regulators of fundamental biological processes, including cell cycle activity (E2F1, glycolysis (HLF, mitochondrial transcription (TFB2M, adipogenesis (PIAS1, neuronal development (TLX3, immune function (IRF1 and vasculogenesis (SOX17, within a skeletal muscle context. However, none of the canonical pro-myogenic transcription factors (MYOD1, MYOG, MYF5, MYF6 and MEF2C were linked to muscle structural gene expression modules. Co-expression values were computed using developing bovine muscle from 60 days post conception (early foetal to 30 months post natal (adulthood for two breeds of cattle, in addition to a nutritional comparison with a third breed. A number of transcriptional landscapes were constructed and integrated into an always correlated landscape. One notable feature was a 'metabolic axis' formed from glycolysis genes at one end, nuclear-encoded mitochondrial protein genes at the other, and centrally tethered by mitochondrially-encoded mitochondrial protein genes. CONCLUSIONS/SIGNIFICANCE: The new module-to-regulator algorithm complements our recently described Regulatory Impact Factor analysis. Together with a simple examination of a co-expression module's contents, these three gene expression approaches are starting to illuminate the in vivo

Co-factors necessary for PPAR mediated transactivation of endogenous target genes

DEFF Research Database (Denmark)

Grøntved, Lars; Nielsen, Ronni; Stunnenberg, Henk

of endogenous target gene in different cell types are elusive. To mutually compare the ability of the PPAR subtypes to activate endogenous target genes in a given cell, PPARa, PPARb/d and PPARg2 were HA tagged and rapidly, equally and synchronously expressed using adenoviral delivery. Within a few hours after...... subtype specific activation of target genes. Accumulating evidence suggests that transcriptional co-factors can function as master regulators for nuclear receptors and impose promoter selectivity. To study co-factor necessity for PPAR mediated transactivation of endogenous target genes, specific co...

Construction and identification of double-gene co-expression vector with radiation-inducible human TRAIL and endostatin

International Nuclear Information System (INIS)

Li Yanbo; Guo Caixia; Gong Pingsheng; Liu Yang; Liangshuo; Wang Hongfang; Wang Jianfeng; Gong Shouliang

2010-01-01

Objective: To construct a recombinant plasmid pshuttle-Egr1-shTRAIL-shES containing tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) and endostatin double genes. Methods: The secretary endostatin gene (shES) fragment was amplified from the pMD19T-endostatin vector by PCR. The shES gene was ligated to pMD19Tand sequenced. Finally, using the gene recombinant technique, the recombinant plasmid pshuttle-Egr1- shTRAIL-shES with radiation-inducible Egr1 promoter, secretary TRAIL and endostatin double-gene was constructed. Results: The sequence of the shES gene was in concordance with that anticipated indicating shES gene was acquired successfully.Moreover, the results acquired by PCR and restrictive digestion identification of the recombinant plasmid pshuttle-Egr1-shTRAIL-shES and all the vectors refered to its construction confirmed that pshuttle-Egr1-shTRAIL-shES was constructed correctly. Conclusion: The radiation-inducible double-gene co-expression vector pshuttle-Egr1-shTRAIL-shES is constructed successfully, which would set the experimental foundation for further study on the anti-tumor effect of TRAIL and endostatin double-gene-radiotherapy and its related mechanisms. (authors)

The Relationship Between Transcript Expression Levels of Nuclear Encoded (TFAM, NRF1 and Mitochondrial Encoded (MT-CO1 Genes in Single Human Oocytes During Oocyte Maturation

Directory of Open Access Journals (Sweden)

Ghaffari Novin M.

2015-06-01

Full Text Available In some cases of infertility in women, human oocytes fail to mature when they reach the metaphase II (MII stage. Mitochondria plays an important role in oocyte maturation. A large number of mitochondrial DNA (mtDNA, copied in oocytes, is essential for providing adenosine triphosphate (ATP during oocyte maturation. The purpose of this study was to identify the relationship between transcript expression levels of the mitochondrial encoded gene (MT-CO1 and two nuclear encoded genes, nuclear respiratory factor 1 (NRF1 and mitochondrial transcription factor A (TFAM in various stages of human oocyte maturation. Nine consenting patients, age 21-35 years old, with male factors were selected for ovarian stimulation and intracytoplasmic sperm injection (ICSI procedures. mRNA levels of mitochondrial- related genes were performed by singlecell TaqMan® quantitative real-time polymerase chain reaction (qRT-PCR. There was no significant relationship between the relative expression levels in germinal vesicle (GV stage oocytes (p = 0.62. On the contrary, a significant relationship was seen between the relative expression levels of TFAM and NRF1 and the MT-CO1 genes at the stages of metaphase I (MI and MII (p = 0.03 and p = 0.002. A relationship exists between the transcript expression levels of TFAM and NRF1, and MT-CO1 genes in various stages of human oocyte maturation.

Effects of experimental muscle pain on muscle activity and co-ordination during static and dynamic motor function.

Science.gov (United States)

Graven-Nielsen, T; Svensson, P; Arendt-Nielsen, L

1997-04-01

The relation between muscle pain, muscle activity, and muscle co-ordination is still controversial. The present human study investigates the influence of experimental muscle pain on resting, static, and dynamic muscle activity. In the resting and static experiments, the electromyography (EMG) activity and the contraction force of m. tibialis anterior were assessed before and after injection of 0.5 ml hypertonic saline (5%) into the same muscle. In the dynamic experiment, injections of 0.5 ml hypertonic saline (5%) were performed into either m. tibialis anterior (TA) or m. gastrocnemius (GA) and the muscle activity and co-ordination were investigated during gait on a treadmill by EMG recordings from m. TA and m. GA. At rest no evidence of EMG hyperactivity was found during muscle pain. The maximal voluntary contraction (MVC) during muscle pain was significantly lower than the control condition (P Fibromyalgia and Myofascial Pain. Elsevier, Amsterdam, 1993, pp. 311-327.) which predicts increased activity of antagonistic muscle and decreased activity of agonistic muscle during experimental and clinical muscle pain.

Encouraging ethical considerations - One important task for a national co-ordinator for nuclear waste disposal

International Nuclear Information System (INIS)

Soederberg, O.

1999-01-01

The paper is a brief description of the role and tasks of the Swedish National Co-ordinator for Nuclear Waste Disposal with special regard to one of his activities encouraging ethical considerations in the nuclear waste management issue. Examples are given of ethical considerations which have emerged during discussions among representatives of municipalities which are affected by the current search for a site for a deep geological repository in Sweden for spent nuclear fuel

Silencing of SARS-CoV spike gene by small interfering RNA in HEK 293T cells

International Nuclear Information System (INIS)

Qin Zhaoling; Zhao Ping; Zhang Xiaolian; Yu Jianguo; Cao Mingmei; Zhao Lanjuan; Luan Jie; Qi Zhongtian

2004-01-01

Two candidate small interfering RNAs (siRNAs) corresponding to severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike gene were designed and in vitro transcribed to explore the possibility of silencing SARS-CoV S gene. The plasmid pEGFP-optS, which contains the codon-optimized SARS-CoV S gene and expresses spike-EGFP fusion protein (S-EGFP) as silencing target and expressing reporter, was transfected with siRNAs into HEK 293T cells. At various time points of posttransfection, the levels of S-EGFP expression and amounts of spike mRNA transcript were detected by fluorescence microscopy, flow cytometry, Western blot, and real-time quantitative PCR, respectively. The results showed that the cells transfected with pEGFP-optS expressed S-EGFP fusion protein at a higher level compared with those transfected with pEGFP-S, which contains wildtype SARS-CoV spike gene sequence. The green fluorescence, mean fluorescence intensity, and SARS-CoV S RNA transcripts were found significantly reduced, and the expression of SARS-CoV S glycoprotein was strongly inhibited in those cells co-transfected with either EGFP- or S-specific siRNAs. Our findings demonstrated that the S-specific siRNAs used in this study were able to specifically and effectively inhibit SARS-CoV S glycoprotein expression in cultured cells through blocking the accumulation of S mRNA, which may provide an approach for studies on the functions of SARS-CoV S gene and development of novel prophylactic or therapeutic agents for SARS-CoV

Co-ordinated research and environmental surveillance programme related to sea disposal of radioactive waste

International Nuclear Information System (INIS)

1996-01-01

The co-ordinated Research and Environmental Surveillance Programme relevant to sea disposal of radioactive waste (CRESP) was created in 1981 in the framework of the 1977 Decision of the OECD Council establishing a Multilateral Consultation and Surveillance Mechanism for Sea Dumping of Radioactive Waste. CRESP was essentially a scientific research programme. Its main objective was to increase the knowledge of processes controlling the transfer of radionuclides in the marine environment, so that safety assessments could be based on more accurate and comprehensive scientific data. From 1986, in response to a request from the Paris Commission, CRESP also considered the scientific aspects of coastal releases. CRESP made it possible to co-ordinate national research activities and generated an important international co-operation in its areas of work. The vast amount of scientific information gathered in this framework increased strongly our knowledge of the impact of radionuclides introduced to the deep sea environment. In particular, CRESP provided the basis for a comprehensive safety analysis of sea dumping operations. This study, published by the NEA in 1985, is still e reference on the subject. In November 1993, the Sixteenth Consultative Meeting of Contracting Parties to the London Convention 1972 voted a total ban on the disposal at sea of radioactive wastes and other radioactive matter. Considering this decision, the conclusions of the 1985 safety analysis, and CRESP's view that new scientific findings are unlikely to alter these conclusions, the NEA Steering Committee for nuclear Energy decided in October 1995 to terminate the programme. The present report summarises the knowledge accumulated within CRESP over its fifteen years of existence. (author)

Functional characterization of a Penicillium chrysogenum mutanase gene induced upon co-cultivation with Bacillus subtilis

NARCIS (Netherlands)

Bajaj, I.; Veiga, T.; Van Dissel, D.; Pronk, J.T.; Daran, J.M.

2014-01-01

Background Microbial gene expression is strongly influenced by environmental growth conditions. Comparison of gene expression under different conditions is frequently used for functional analysis and to unravel regulatory networks, however, gene expression responses to co-cultivation with other

A Network Approach of Gene Co-expression in the Zea mays/Aspergillus flavus Pathosystem to Map Host/Pathogen Interaction Pathways

Science.gov (United States)

Musungu, Bryan M.; Bhatnagar, Deepak; Brown, Robert L.; Payne, Gary A.; OBrian, Greg; Fakhoury, Ahmad M.; Geisler, Matt

2016-01-01

A gene co-expression network (GEN) was generated using a dual RNA-seq study with the fungal pathogen Aspergillus flavus and its plant host Zea mays during the initial 3 days of infection. The analysis deciphered novel pathways and mapped genes of interest in both organisms during the infection. This network revealed a high degree of connectivity in many of the previously recognized pathways in Z. mays such as jasmonic acid, ethylene, and reactive oxygen species (ROS). For the pathogen A. flavus, a link between aflatoxin production and vesicular transport was identified within the network. There was significant interspecies correlation of expression between Z. mays and A. flavus for a subset of 104 Z. mays, and 1942 A. flavus genes. This resulted in an interspecies subnetwork enriched in multiple Z. mays genes involved in the production of ROS. In addition to the ROS from Z. mays, there was enrichment in the vesicular transport pathways and the aflatoxin pathway for A. flavus. Included in these genes, a key aflatoxin cluster regulator, AflS, was found to be co-regulated with multiple Z. mays ROS producing genes within the network, suggesting AflS may be monitoring host ROS levels. The entire GEN for both host and pathogen, and the subset of interspecies correlations, is presented as a tool for hypothesis generation and discovery for events in the early stages of fungal infection of Z. mays by A. flavus. PMID:27917194

A Network Approach of Gene Co-expression in the Zea mays/Aspergillus flavus Pathosystem to Map Host/Pathogen Interaction Pathways.

Science.gov (United States)

Musungu, Bryan M; Bhatnagar, Deepak; Brown, Robert L; Payne, Gary A; OBrian, Greg; Fakhoury, Ahmad M; Geisler, Matt

2016-01-01

A gene co-expression network (GEN) was generated using a dual RNA-seq study with the fungal pathogen Aspergillus flavus and its plant host Zea mays during the initial 3 days of infection. The analysis deciphered novel pathways and mapped genes of interest in both organisms during the infection. This network revealed a high degree of connectivity in many of the previously recognized pathways in Z. mays such as jasmonic acid, ethylene, and reactive oxygen species (ROS). For the pathogen A. flavus , a link between aflatoxin production and vesicular transport was identified within the network. There was significant interspecies correlation of expression between Z. mays and A. flavus for a subset of 104 Z. mays , and 1942 A. flavus genes. This resulted in an interspecies subnetwork enriched in multiple Z. mays genes involved in the production of ROS. In addition to the ROS from Z. mays , there was enrichment in the vesicular transport pathways and the aflatoxin pathway for A. flavus . Included in these genes, a key aflatoxin cluster regulator, AflS, was found to be co-regulated with multiple Z. mays ROS producing genes within the network, suggesting AflS may be monitoring host ROS levels. The entire GEN for both host and pathogen, and the subset of interspecies correlations, is presented as a tool for hypothesis generation and discovery for events in the early stages of fungal infection of Z. mays by A. flavus .

Comparison of co-expression measures: mutual information, correlation, and model based indices.

Science.gov (United States)

Song, Lin; Langfelder, Peter; Horvath, Steve

2012-12-09

Co-expression measures are often used to define networks among genes. Mutual information (MI) is often used as a generalized correlation measure. It is not clear how much MI adds beyond standard (robust) correlation measures or regression model based association measures. Further, it is important to assess what transformations of these and other co-expression measures lead to biologically meaningful modules (clusters of genes). We provide a comprehensive comparison between mutual information and several correlation measures in 8 empirical data sets and in simulations. We also study different approaches for transforming an adjacency matrix, e.g. using the topological overlap measure. Overall, we confirm close relationships between MI and correlation in all data sets which reflects the fact that most gene pairs satisfy linear or monotonic relationships. We discuss rare situations when the two measures disagree. We also compare correlation and MI based approaches when it comes to defining co-expression network modules. We show that a robust measure of correlation (the biweight midcorrelation transformed via the topological overlap transformation) leads to modules that are superior to MI based modules and maximal information coefficient (MIC) based modules in terms of gene ontology enrichment. We present a function that relates correlation to mutual information which can be used to approximate the mutual information from the corresponding correlation coefficient. We propose the use of polynomial or spline regression models as an alternative to MI for capturing non-linear relationships between quantitative variables. The biweight midcorrelation outperforms MI in terms of elucidating gene pairwise relationships. Coupled with the topological overlap matrix transformation, it often leads to more significantly enriched co-expression modules. Spline and polynomial networks form attractive alternatives to MI in case of non-linear relationships. Our results indicate that MI

Gene expression and gene therapy imaging

International Nuclear Information System (INIS)

Rome, Claire; Couillaud, Franck; Moonen, Chrit T.W.

2007-01-01

The fast growing field of molecular imaging has achieved major advances in imaging gene expression, an important element of gene therapy. Gene expression imaging is based on specific probes or contrast agents that allow either direct or indirect spatio-temporal evaluation of gene expression. Direct evaluation is possible with, for example, contrast agents that bind directly to a specific target (e.g., receptor). Indirect evaluation may be achieved by using specific substrate probes for a target enzyme. The use of marker genes, also called reporter genes, is an essential element of MI approaches for gene expression in gene therapy. The marker gene may not have a therapeutic role itself, but by coupling the marker gene to a therapeutic gene, expression of the marker gene reports on the expression of the therapeutic gene. Nuclear medicine and optical approaches are highly sensitive (detection of probes in the picomolar range), whereas MRI and ultrasound imaging are less sensitive and require amplification techniques and/or accumulation of contrast agents in enlarged contrast particles. Recently developed MI techniques are particularly relevant for gene therapy. Amongst these are the possibility to track gene therapy vectors such as stem cells, and the techniques that allow spatiotemporal control of gene expression by non-invasive heating (with MRI guided focused ultrasound) and the use of temperature sensitive promoters. (orig.)

ESR1 is co-expressed with closely adjacent uncharacterised genes spanning a breast cancer susceptibility locus at 6q25.1.

Directory of Open Access Journals (Sweden)

Anita K Dunbier

2011-04-01

Full Text Available Approximately 80% of human breast carcinomas present as oestrogen receptor α-positive (ER+ve disease, and ER status is a critical factor in treatment decision-making. Recently, single nucleotide polymorphisms (SNPs in the region immediately upstream of the ER gene (ESR1 on 6q25.1 have been associated with breast cancer risk. Our investigation of factors associated with the level of expression of ESR1 in ER+ve tumours has revealed unexpected associations between genes in this region and ESR1 expression that are important to consider in studies of the genetic causes of breast cancer risk. RNA from tumour biopsies taken from 104 postmenopausal women before and after 2 weeks treatment with an aromatase (oestrogen synthase inhibitor was analyzed on Illumina 48K microarrays. Multiple-testing corrected Spearman correlation revealed that three previously uncharacterized open reading frames (ORFs located immediately upstream of ESR1, C6ORF96, C6ORF97, and C6ORF211 were highly correlated with ESR1 (Rs =  0.67, 0.64, and 0.55 respectively, FDR<1 × 10(-7. Publicly available datasets confirmed this relationship in other groups of ER+ve tumours. DNA copy number changes did not account for the correlations. The correlations were maintained in cultured cells. An ERα antagonist did not affect the ORFs' expression or their correlation with ESR1, suggesting their transcriptional co-activation is not directly mediated by ERα. siRNA inhibition of C6ORF211 suppressed proliferation in MCF7 cells, and C6ORF211 positively correlated with a proliferation metagene in tumours. In contrast, C6ORF97 expression correlated negatively with the metagene and predicted for improved disease-free survival in a tamoxifen-treated published dataset, independently of ESR1. Our observations suggest that some of the biological effects previously attributed to ER could be mediated and/or modified by these co-expressed genes. The co-expression and function of these genes may be

Co-Option and De Novo Gene Evolution Underlie Molluscan Shell Diversity

Science.gov (United States)

Aguilera, Felipe; McDougall, Carmel

2017-01-01

Abstract Molluscs fabricate shells of incredible diversity and complexity by localized secretions from the dorsal epithelium of the mantle. Although distantly related molluscs express remarkably different secreted gene products, it remains unclear if the evolution of shell structure and pattern is underpinned by the differential co-option of conserved genes or the integration of lineage-specific genes into the mantle regulatory program. To address this, we compare the mantle transcriptomes of 11 bivalves and gastropods of varying relatedness. We find that each species, including four Pinctada (pearl oyster) species that diverged within the last 20 Ma, expresses a unique mantle secretome. Lineage- or species-specific genes comprise a large proportion of each species’ mantle secretome. A majority of these secreted proteins have unique domain architectures that include repetitive, low complexity domains (RLCDs), which evolve rapidly, and have a proclivity to expand, contract and rearrange in the genome. There are also a large number of secretome genes expressed in the mantle that arose before the origin of gastropods and bivalves. Each species expresses a unique set of these more ancient genes consistent with their independent co-option into these mantle gene regulatory networks. From this analysis, we infer lineage-specific secretomes underlie shell diversity, and include both rapidly evolving RLCD-containing proteins, and the continual recruitment and loss of both ancient and recently evolved genes into the periphery of the regulatory network controlling gene expression in the mantle epithelium. PMID:28053006

Detecting microRNA activity from gene expression data

LENUS (Irish Health Repository)

Madden, Stephen F

2010-05-18

Abstract Background MicroRNAs (miRNAs) are non-coding RNAs that regulate gene expression by binding to the messenger RNA (mRNA) of protein coding genes. They control gene expression by either inhibiting translation or inducing mRNA degradation. A number of computational techniques have been developed to identify the targets of miRNAs. In this study we used predicted miRNA-gene interactions to analyse mRNA gene expression microarray data to predict miRNAs associated with particular diseases or conditions. Results Here we combine correspondence analysis, between group analysis and co-inertia analysis (CIA) to determine which miRNAs are associated with differences in gene expression levels in microarray data sets. Using a database of miRNA target predictions from TargetScan, TargetScanS, PicTar4way PicTar5way, and miRanda and combining these data with gene expression levels from sets of microarrays, this method produces a ranked list of miRNAs associated with a specified split in samples. We applied this to three different microarray datasets, a papillary thyroid carcinoma dataset, an in-house dataset of lipopolysaccharide treated mouse macrophages, and a multi-tissue dataset. In each case we were able to identified miRNAs of biological importance. Conclusions We describe a technique to integrate gene expression data and miRNA target predictions from multiple sources.

Detecting microRNA activity from gene expression data.

LENUS (Irish Health Repository)

Madden, Stephen F

2010-01-01

BACKGROUND: MicroRNAs (miRNAs) are non-coding RNAs that regulate gene expression by binding to the messenger RNA (mRNA) of protein coding genes. They control gene expression by either inhibiting translation or inducing mRNA degradation. A number of computational techniques have been developed to identify the targets of miRNAs. In this study we used predicted miRNA-gene interactions to analyse mRNA gene expression microarray data to predict miRNAs associated with particular diseases or conditions. RESULTS: Here we combine correspondence analysis, between group analysis and co-inertia analysis (CIA) to determine which miRNAs are associated with differences in gene expression levels in microarray data sets. Using a database of miRNA target predictions from TargetScan, TargetScanS, PicTar4way PicTar5way, and miRanda and combining these data with gene expression levels from sets of microarrays, this method produces a ranked list of miRNAs associated with a specified split in samples. We applied this to three different microarray datasets, a papillary thyroid carcinoma dataset, an in-house dataset of lipopolysaccharide treated mouse macrophages, and a multi-tissue dataset. In each case we were able to identified miRNAs of biological importance. CONCLUSIONS: We describe a technique to integrate gene expression data and miRNA target predictions from multiple sources.

Twenty-Third Report of the Administrative Committee on Co-ordination to the Economic and Social Council of the United Nations

Energy Technology Data Exchange (ETDEWEB)

NONE

1959-07-09

In accordance with Article XI of the Relationship Agreement between the Agency and the United Nations, the Agency is participating in the work of the Administrative Committee on Co-ordination (ACC) and of certain of its subsidiary bodies.

Co-expression of the Thermotoga neapolitana aglB gene with an upstream 3'-coding fragment of the malG gene improves enzymatic characteristics of recombinant AglB cyclomaltodextrinase.

Science.gov (United States)

Lunina, Natalia A; Agafonova, Elena V; Chekanovskaya, Lyudmila A; Dvortsov, Igor A; Berezina, Oksana V; Shedova, Ekaterina N; Kostrov, Sergey V; Velikodvorskaya, Galina A

2007-07-01

A cluster of Thermotoga neapolitana genes participating in starch degradation includes the malG gene of sugar transport protein and the aglB gene of cyclomaltodextrinase. The start and stop codons of these genes share a common overlapping sequence, aTGAtg. Here, we compared properties of expression products of three different constructs with aglB from T. neapolitana. The first expression vector contained the aglB gene linked to an upstream 90-bp 3'-terminal region of the malG gene with the stop codon overlapping with the start codon of aglB. The second construct included the isolated coding sequence of aglB with two tandem potential start codons. The expression product of this construct in Escherichia coli had two tandem Met residues at its N terminus and was characterized by low thermostability and high tendency to aggregate. In contrast, co-expression of aglB and the 3'-terminal region of malG (the first construct) resulted in AglB with only one N-terminal Met residue and a much higher specific activity of cyclomaltodextrinase. Moreover, the enzyme expressed by such a construct was more thermostable and less prone to aggregation. The third construct was the same as the second one except that it contained only one ATG start codon. The product of its expression had kinetic and other properties similar to those of the enzyme with only one N-terminal Met residue.

Genes associated with thermosensitive genic male sterility in rice identified by comparative expression profiling.

Science.gov (United States)

Pan, Yufang; Li, Qiaofeng; Wang, Zhizheng; Wang, Yang; Ma, Rui; Zhu, Lili; He, Guangcun; Chen, Rongzhi

2014-12-16

Thermosensitive genic male sterile (TGMS) lines and photoperiod-sensitive genic male sterile (PGMS) lines have been successfully used in hybridization to improve rice yields. However, the molecular mechanisms underlying male sterility transitions in most PGMS/TGMS rice lines are unclear. In the recently developed TGMS-Co27 line, the male sterility is based on co-suppression of a UDP-glucose pyrophosphorylase gene (Ugp1), but further study is needed to fully elucidate the molecular mechanisms involved. Microarray-based transcriptome profiling of TGMS-Co27 and wild-type Hejiang 19 (H1493) plants grown at high and low temperatures revealed that 15462 probe sets representing 8303 genes were differentially expressed in the two lines, under the two conditions, or both. Environmental factors strongly affected global gene expression. Some genes important for pollen development were strongly repressed in TGMS-Co27 at high temperature. More significantly, series-cluster analysis of differentially expressed genes (DEGs) between TGMS-Co27 plants grown under the two conditions showed that low temperature induced the expression of a gene cluster. This cluster was found to be essential for sterility transition. It includes many meiosis stage-related genes that are probably important for thermosensitive male sterility in TGMS-Co27, inter alia: Arg/Ser-rich domain (RS)-containing zinc finger proteins, polypyrimidine tract-binding proteins (PTBs), DEAD/DEAH box RNA helicases, ZOS (C2H2 zinc finger proteins of Oryza sativa), at least one polyadenylate-binding protein and some other RNA recognition motif (RRM) domain-containing proteins involved in post-transcriptional processes, eukaryotic initiation factor 5B (eIF5B), ribosomal proteins (L37, L1p/L10e, L27 and L24), aminoacyl-tRNA synthetases (ARSs), eukaryotic elongation factor Tu (eEF-Tu) and a peptide chain release factor protein involved in translation. The differential expression of 12 DEGs that are important for pollen

Genome-wide expression of transcriptomes and their co-expression pattern in subtropical maize (Zea mays L. under waterlogging stress.

Directory of Open Access Journals (Sweden)

Nepolean Thirunavukkarasu

Full Text Available Waterlogging causes extensive damage to maize crops in tropical and subtropical regions. The identification of tolerance genes and their interactions at the molecular level will be helpful to engineer tolerant genotypes. A whole-genome transcriptome assay revealed the specific role of genes in response to waterlogging stress in susceptible and tolerant genotypes. Genes involved in the synthesis of ethylene and auxin, cell wall metabolism, activation of G-proteins and formation of aerenchyma and adventitious roots, were upregulated in the tolerant genotype. Many transcription factors, particularly ERFs, MYB, HSPs, MAPK, and LOB-domain protein were involved in regulation of these traits. Genes responsible for scavenging of ROS generated under stress were expressed along with those involved in carbohydrate metabolism. The physical locations of 21 genes expressed in the tolerant genotype were found to correspond with the marker intervals of known QTLs responsible for development of adaptive traits. Among the candidate genes, most showed synteny with genes of sorghum and foxtail millet. Co-expression analysis of 528 microarray samples including 16 samples from the present study generated seven functional modules each in the two genotypes, with differing characteristics. In the tolerant genotype, stress genes were co-expressed along with peroxidase and fermentation pathway genes.

Characterization of claustral neurons by comparative gene expression profiling and dye-injection analyses

Directory of Open Access Journals (Sweden)

Akiya eWatakabe

2014-05-01

Full Text Available The identity of the claustrum as a part of cerebral cortex, and in particular of the adjacent insular cortex, has been investigated by connectivity features and patterns of gene expression. In the present paper, we mapped the cortical and claustral expression of several cortical genes in rodent and macaque monkey brains (nurr1, latexin, cux2, and netrinG2 to further assess shared features between cortex and claustrum. In mice, these genes were densely expressed in the claustrum, but very sparsely in the cortex and not present in the striatum. To test whether the cortical vs. claustral cell types can be distinguished by co-expression of these genes, we performed a panel of double ISH in mouse and macaque brain. NetrinG2 and nurr1 genes were co-expressed across entire cortex and claustrum, but cux2 and nurr1 were co-expressed only in the insular cortex and claustrum. Latexin was expressed, in the macaque, only in the claustrum. The nurr1+ claustral neurons expressed VGluT1, a marker for cortical glutamatergic cells and send cortical projections. Taken together, our data suggest a partial commonality between claustral neurons and a subtype of cortical neurons in the monkey brain. Moreover, in the embryonic (E110 macaque brain, many nurr1+ neurons were scattered in the white matter between the claustrum and the insular cortex, possibly representing their migratory history. In a second set of experiments, we injected Lucifer Yellow intracellularly in mouse and rat slices to investigate whether dendrites of insular and claustral neurons can cross the border of the two brain regions. Dendrites of claustral neurons did not invade the overlying insular territory. In summary, gene expression profile of the claustrum is similar to that of the neocortex, in both rodent and macaque brains, but with modifications in density of expression and cellular co-localization of specific genes.

Gene expression in rat striatum following carbon monoxide poisoning

Directory of Open Access Journals (Sweden)

Shuichi Hara

2017-06-01

Full Text Available Carbon monoxide (CO poisoning causes brain damage, which is attenuated by treatment with hydrogen [1,2], a scavenger selective to hydroxyl radical (·≡OH [3]. This suggests a role of ·≡OH in brain damage due to CO poisoning. Studies have shown strong enhancement of ·≡OH production in rat striatum by severe CO poisoning with a blood carboxyhemoglobin (COHb level >70% due to 3000 ppm CO, but not less severe CO poisoning with a blood COHb level at approximately 50% due to 1000 ppm CO [4]. Interestingly, 5% O2 causes hypoxia comparable with that by 3000 ppm CO and produces much less •OH than 3000 ppm CO does [4]. In addition, cAMP production in parallel with ·≡OH production [5] might contribute to ·≡OH production [6]. It is likely that mechanisms other than hypoxia contribute to brain damage due to CO poisoning [7]. To search for the mechanisms, we examined the effects of 1000 ppm CO, 3000 ppm CO and 5% O2 on gene expression in rat striatum. All array data have been deposited in the Gene Expression Omnibus (GEO database under accession number GSE94780.

Exploring Plant Co-Expression and Gene-Gene Interactions with CORNET 3.0.

Science.gov (United States)

Van Bel, Michiel; Coppens, Frederik

2017-01-01

Selecting and filtering a reference expression and interaction dataset when studying specific pathways and regulatory interactions can be a very time-consuming and error-prone task. In order to reduce the duplicated efforts required to amass such datasets, we have created the CORNET (CORrelation NETworks) platform which allows for easy access to a wide variety of data types: coexpression data, protein-protein interactions, regulatory interactions, and functional annotations. The CORNET platform outputs its results in either text format or through the Cytoscape framework, which is automatically launched by the CORNET website.CORNET 3.0 is the third iteration of the web platform designed for the user exploration of the coexpression space of plant genomes, with a focus on the model species Arabidopsis thaliana. Here we describe the platform: the tools, data, and best practices when using the platform. We indicate how the platform can be used to infer networks from a set of input genes, such as upregulated genes from an expression experiment. By exploring the network, new target and regulator genes can be discovered, allowing for follow-up experiments and more in-depth study. We also indicate how to avoid common pitfalls when evaluating the networks and how to avoid over interpretation of the results.All CORNET versions are available at http://bioinformatics.psb.ugent.be/cornet/ .

Gene expression and adaptive noncoding changes during human evolution.

Science.gov (United States)

Babbitt, Courtney C; Haygood, Ralph; Nielsen, William J; Wray, Gregory A

2017-06-05

Despite evidence for adaptive changes in both gene expression and non-protein-coding, putatively regulatory regions of the genome during human evolution, the relationship between gene expression and adaptive changes in cis-regulatory regions remains unclear. Here we present new measurements of gene expression in five tissues of humans and chimpanzees, and use them to assess this relationship. We then compare our results with previous studies of adaptive noncoding changes, analyzing correlations at the level of gene ontology groups, in order to gain statistical power to detect correlations. Consistent with previous studies, we find little correlation between gene expression and adaptive noncoding changes at the level of individual genes; however, we do find significant correlations at the level of biological function ontology groups. The types of function include processes regulated by specific transcription factors, responses to genetic or chemical perturbations, and differentiation of cell types within the immune system. Among functional categories co-enriched with both differential expression and noncoding adaptation, prominent themes include cancer, particularly epithelial cancers, and neural development and function.

Some Problems of Rocket-Space Vehicles' Characteristics co- ordination

Science.gov (United States)

Sergienko, Alexander A.

2002-01-01

of the XX century suffered a reverse. The designers of the United States' firms and enterprises of aviation and rocket-space industry (Boeing, Rocketdyne, Lockheed Martin, McDonnell Douglas, Rockwell, etc.) and NASA (Marshall Space Flight Center, Johnson Space Center, Langley Research Center and Lewis Research Center and others) could not correctly co-ordinate the characteristics of a propulsion system and a space vehicle for elaboration of the "Single-Stage-To-Orbit" reusable vehicle (SSTO) as an integral whole system, which is would able to inject a payload into an orbit and to return back on the Earth. jet nozzle design as well as the choice of propulsion system characteristics, ensuring the high ballistic efficiency, are considered in the present report. The efficiency criterions for the engine and launch system parameters optimization are discussed. The new methods of the nozzle block optimal parameters' choice for the satisfaction of the object task of flight are suggested. The family of SSTO with a payload mass from 5 to 20 ton and initial weight under 800 ton is considered.

How protein kinases co-ordinate mitosis in animal cells.

Science.gov (United States)

Ma, Hoi Tang; Poon, Randy Y C

2011-04-01

Mitosis is associated with profound changes in cell physiology and a spectacular surge in protein phosphorylation. To accomplish these, a remarkably large portion of the kinome is involved in the process. In the present review, we will focus on classic mitotic kinases, such as cyclin-dependent kinases, Polo-like kinases and Aurora kinases, as well as more recently characterized players such as NIMA (never in mitosis in Aspergillus nidulans)-related kinases, Greatwall and Haspin. Together, these kinases co-ordinate the proper timing and fidelity of processes including centrosomal functions, spindle assembly and microtubule-kinetochore attachment, as well as sister chromatid separation and cytokinesis. A recurrent theme of the mitotic kinase network is the prevalence of elaborated feedback loops that ensure bistable conditions. Sequential phosphorylation and priming phosphorylation on substrates are also frequently employed. Another important concept is the role of scaffolds, such as centrosomes for protein kinases during mitosis. Elucidating the entire repertoire of mitotic kinases, their functions, regulation and interactions is critical for our understanding of normal cell growth and in diseases such as cancers.

ICan: an integrated co-alteration network to identify ovarian cancer-related genes.

Science.gov (United States)

Zhou, Yuanshuai; Liu, Yongjing; Li, Kening; Zhang, Rui; Qiu, Fujun; Zhao, Ning; Xu, Yan

2015-01-01

Over the last decade, an increasing number of integrative studies on cancer-related genes have been published. Integrative analyses aim to overcome the limitation of a single data type, and provide a more complete view of carcinogenesis. The vast majority of these studies used sample-matched data of gene expression and copy number to investigate the impact of copy number alteration on gene expression, and to predict and prioritize candidate oncogenes and tumor suppressor genes. However, correlations between genes were neglected in these studies. Our work aimed to evaluate the co-alteration of copy number, methylation and expression, allowing us to identify cancer-related genes and essential functional modules in cancer. We built the Integrated Co-alteration network (ICan) based on multi-omics data, and analyzed the network to uncover cancer-related genes. After comparison with random networks, we identified 155 ovarian cancer-related genes, including well-known (TP53, BRCA1, RB1 and PTEN) and also novel cancer-related genes, such as PDPN and EphA2. We compared the results with a conventional method: CNAmet, and obtained a significantly better area under the curve value (ICan: 0.8179, CNAmet: 0.5183). In this paper, we describe a framework to find cancer-related genes based on an Integrated Co-alteration network. Our results proved that ICan could precisely identify candidate cancer genes and provide increased mechanistic understanding of carcinogenesis. This work suggested a new research direction for biological network analyses involving multi-omics data.

Applied research on air pollution using nuclear-related analytical techniques. Report on the second research co-ordination meeting

Energy Technology Data Exchange (ETDEWEB)

NONE

1995-07-01

A co-ordinated research programme (CRP) on applied research on air pollution using nuclear-related techniques is a global CRP which started in 1992, and is scheduled to run until early 1997. The purpose of this CRP is to promote the use of nuclear analytical techniques in air pollution studies, e.g. NAA, XRF, and PIXE for the analysis of toxic and other trace elements in air particulate matter. The main purposes of the core programme are i) to support the use of nuclear and nuclear-related analytical techniques for research and monitoring studies on air pollution, ii) to identify major sources of air pollution affecting each of the participating countries with particular reference to toxic heavy metals, and iii) to obtain comparative data on pollution levels in areas of high pollution (e.g. a city centre or a populated area downwind of a large pollution source) and low pollution (e.g. rural area). This document reports the discussions held during the second Research Co-ordination Meeting (RCM) for the CRP which took place at ANSTO in Menai, Australia. (author)

Applied research on air pollution using nuclear-related analytical techniques. Report on the second research co-ordination meeting

International Nuclear Information System (INIS)

1995-01-01

A co-ordinated research programme (CRP) on applied research on air pollution using nuclear-related techniques is a global CRP which started in 1992, and is scheduled to run until early 1997. The purpose of this CRP is to promote the use of nuclear analytical techniques in air pollution studies, e.g. NAA, XRF, and PIXE for the analysis of toxic and other trace elements in air particulate matter. The main purposes of the core programme are i) to support the use of nuclear and nuclear-related analytical techniques for research and monitoring studies on air pollution, ii) to identify major sources of air pollution affecting each of the participating countries with particular reference to toxic heavy metals, and iii) to obtain comparative data on pollution levels in areas of high pollution (e.g. a city centre or a populated area downwind of a large pollution source) and low pollution (e.g. rural area). This document reports the discussions held during the second Research Co-ordination Meeting (RCM) for the CRP which took place at ANSTO in Menai, Australia. (author)

Gene expression

International Nuclear Information System (INIS)

Hildebrand, C.E.; Crawford, B.D.; Walters, R.A.; Enger, M.D.

1983-01-01

We prepared probes for isolating functional pieces of the metallothionein locus. The probes enabled a variety of experiments, eventually revealing two mechanisms for metallothionein gene expression, the order of the DNA coding units at the locus, and the location of the gene site in its chromosome. Once the switch regulating metallothionein synthesis was located, it could be joined by recombinant DNA methods to other, unrelated genes, then reintroduced into cells by gene-transfer techniques. The expression of these recombinant genes could then be induced by exposing the cells to Zn 2+ or Cd 2+ . We would thus take advantage of the clearly defined switching properties of the metallothionein gene to manipulate the expression of other, perhaps normally constitutive, genes. Already, despite an incomplete understanding of how the regulatory switch of the metallothionein locus operates, such experiments have been performed successfully

Handbook for the planning, co-ordination and evaluation of emergency exercises in nuclear power plants

International Nuclear Information System (INIS)

Schmidtborn, I.; Bath, N.

1999-01-01

The efficiency of the on-site emergency organization in German nuclear power plants is tested regularly through emergency exercises. To achieve federal harmonization on a high level of quality a handbook for the planning, co-ordination and evaluation of such exercises has been developed in the frame of the regulatory investigation programme. In this handbook requirements are set out for emergency training. Key elements are a modular structure, rules to be observed and guidance for post-exercise evaluation. (orig.) [de

Guidance for RNA-seq co-expression network construction and analysis: safety in numbers.

Science.gov (United States)

Ballouz, S; Verleyen, W; Gillis, J

2015-07-01

RNA-seq co-expression analysis is in its infancy and reasonable practices remain poorly defined. We assessed a variety of RNA-seq expression data to determine factors affecting functional connectivity and topology in co-expression networks. We examine RNA-seq co-expression data generated from 1970 RNA-seq samples using a Guilt-By-Association framework, in which genes are assessed for the tendency of co-expression to reflect shared function. Minimal experimental criteria to obtain performance on par with microarrays were >20 samples with read depth >10 M per sample. While the aggregate network constructed shows good performance (area under the receiver operator characteristic curve ∼0.71), the dependency on number of experiments used is nearly identical to that present in microarrays, suggesting thousands of samples are required to obtain 'gold-standard' co-expression. We find a major topological difference between RNA-seq and microarray co-expression in the form of low overlaps between hub-like genes from each network due to changes in the correlation of expression noise within each technology. jgillis@cshl.edu or sballouz@cshl.edu Networks are available at: http://gillislab.labsites.cshl.edu/supplements/rna-seq-networks/ and supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

TBLR1 regulates the expression of nuclear hormone receptor co-repressors

Directory of Open Access Journals (Sweden)

Brown Stuart

2006-08-01

Full Text Available Abstract Background Transcription is regulated by a complex interaction of activators and repressors. The effectors of repression are large multimeric complexes which contain both the repressor proteins that bind to transcription factors and a number of co-repressors that actually mediate transcriptional silencing either by inhibiting the basal transcription machinery or by recruiting chromatin-modifying enzymes. Results TBLR1 [GenBank: NM024665] is a co-repressor of nuclear hormone transcription factors. A single highly conserved gene encodes a small family of protein molecules. Different isoforms are produced by differential exon utilization. Although the ORF of the predominant form contains only 1545 bp, the human gene occupies ~200 kb of genomic DNA on chromosome 3q and contains 16 exons. The genomic sequence overlaps with the putative DC42 [GenBank: NM030921] locus. The murine homologue is structurally similar and is also located on Chromosome 3. TBLR1 is closely related (79% homology at the mRNA level to TBL1X and TBL1Y, which are located on Chromosomes X and Y. The expression of TBLR1 overlaps but is distinct from that of TBL1. An alternatively spliced form of TBLR1 has been demonstrated in human material and it too has an unique pattern of expression. TBLR1 and the homologous genes interact with proteins that regulate the nuclear hormone receptor family of transcription factors. In resting cells TBLR1 is primarily cytoplasmic but after perturbation the protein translocates to the nucleus. TBLR1 co-precipitates with SMRT, a co-repressor of nuclear hormone receptors, and co-precipitates in complexes immunoprecipitated by antiserum to HDAC3. Cells engineered to over express either TBLR1 or N- and C-terminal deletion variants, have elevated levels of endogenous N-CoR. Co-transfection of TBLR1 and SMRT results in increased expression of SMRT. This co-repressor undergoes ubiquitin-mediated degradation and we suggest that the stabilization of

Homeobox gene expression in Brachiopoda

DEFF Research Database (Denmark)

Altenburger, Andreas; Martinez, Pedro; Wanninger, Andreas

2011-01-01

(ectoderm) specification with co-opted functions in notochord formation in chordates and left/right determination in ambulacrarians and vertebrates. The caudal ortholog, TtrCdx, is first expressed in the ectoderm of the gastrulating embryo in the posterior region of the blastopore. Its expression stays......The molecular control that underlies brachiopod ontogeny is largely unknown. In order to contribute to this issue we analyzed the expression pattern of two homeobox containing genes, Not and Cdx, during development of the rhynchonelliform (i.e., articulate) brachiopod Terebratalia transversa...... completion of larval development, which is marked by a three-lobed body with larval setae. Expression starts at gastrulation in two areas lateral to the blastopore and subsequently extends over the animal pole of the gastrula. With elongation of the gastrula, expression at the animal pole narrows to a small...

Elevated CO2 increases R gene-dependent resistance of Medicago truncatula against the pea aphid by up-regulating a heat shock gene.

Science.gov (United States)

Sun, Yucheng; Guo, Huijuan; Yuan, Erliang; Ge, Feng

2018-03-01

Resistance against pathogens and herbivorous insects in many plant results from the expression of resistance (R) genes. Few reports, however, have considered the effects of elevated CO 2 on R gene-based resistance in plants. The current study determined the responses of two near isogenic Medicago truncatula genotypes (Jester has an R gene and A17 does not) to the pea aphid and elevated CO 2 in open-top chambers in the field. Aphid abundance, mean relative growth rate and feeding efficiency were increased by elevated CO 2 on A17 plants but were reduced on Jester plants. According to proteomic and gene expression data, elevated CO 2 enhanced pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) but decreased the effector-triggered immunity (ETI) in aphid-infested A17 plants. For aphid-infested Jester plants, by contrast, elevated CO 2 enhanced the ETI-related heat shock protein (HSP) 90 and its co-chaperones, the jasmonic acid (JA) signaling pathway, and ubiquitin-mediated proteolysis. In a loss-of-function experiment, silencing of the HSP90 gene in Jester plants impaired the JA signaling pathway and ubiquitin-mediated proteolysis against the aphid under ambient CO 2 , and negated the increased resistance against the aphid under elevated CO 2 . Our results suggest that increases in expression of HSP90 are responsible for the enhanced resistance against the aphid under elevated CO 2 . © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Differential gene expression in primary fibroblasts induced by proton and cobalt-60 beam irradiation

DEFF Research Database (Denmark)

Nielsen, Steffen; Bassler, Niels; Grzanka, Leszek

2017-01-01

profile: entrance, mid-SOBP and at the SOBP distal edge. Dose was delivered in three fractions × 3.5 Gy(RBE) (RBE 1.1). Cobalt-60 (Co-60) irradiation was used as reference. Real-time qPCR was performed to determine gene expression levels for 17 genes associated with inflammation response, fibrosis...... and angiogenesis. RESULTS: Differences in median gene expression levels were observed for multiple genes such as IL6, IL8 and CXCL12. Median IL6 expression was 30%, 24% and 47% lower in entrance, mid-SOBP and SOBP distal edge groups than in Co-60 irradiated cells. No genes were found to be oppositely regulated...... fibroblast cultures. Inflammatory factors were generally less extensively upregulated by proton irradiation compared with Co-60 photon irradiation. These effects may possibly influence the development of normal tissue damage in patients treated with proton beam therapy....

Global similarity and local divergence in human and mouse gene co-expression networks

Directory of Open Access Journals (Sweden)

Koonin Eugene V

2006-09-01

Full Text Available Abstract Background A genome-wide comparative analysis of human and mouse gene expression patterns was performed in order to evaluate the evolutionary divergence of mammalian gene expression. Tissue-specific expression profiles were analyzed for 9,105 human-mouse orthologous gene pairs across 28 tissues. Expression profiles were resolved into species-specific coexpression networks, and the topological properties of the networks were compared between species. Results At the global level, the topological properties of the human and mouse gene coexpression networks are, essentially, identical. For instance, both networks have topologies with small-world and scale-free properties as well as closely similar average node degrees, clustering coefficients, and path lengths. However, the human and mouse coexpression networks are highly divergent at the local level: only a small fraction ( Conclusion The dissonance between global versus local network divergence suggests that the interspecies similarity of the global network properties is of limited biological significance, at best, and that the biologically relevant aspects of the architectures of gene coexpression are specific and particular, rather than universal. Nevertheless, there is substantial evolutionary conservation of the local network structure which is compatible with the notion that gene coexpression networks are subject to purifying selection.

Ebola virus infection induces irregular dendritic cell gene expression.

Science.gov (United States)

Melanson, Vanessa R; Kalina, Warren V; Williams, Priscilla

2015-02-01

Filoviruses subvert the human immune system in part by infecting and replicating in dendritic cells (DCs). Using gene arrays, a phenotypic profile of filovirus infection in human monocyte-derived DCs was assessed. Monocytes from human donors were cultured in GM-CSF and IL-4 and were infected with Ebola virus Kikwit variant for up to 48 h. Extracted DC RNA was analyzed on SuperArray's Dendritic and Antigen Presenting Cell Oligo GEArray and compared to uninfected controls. Infected DCs exhibited increased expression of cytokine, chemokine, antiviral, and anti-apoptotic genes not seen in uninfected controls. Significant increases of intracellular antiviral and MHC I and II genes were also noted in EBOV-infected DCs. However, infected DCs failed to show any significant difference in co-stimulatory T-cell gene expression from uninfected DCs. Moreover, several chemokine genes were activated, but there was sparse expression of chemokine receptors that enabled activated DCs to home to lymph nodes. Overall, statistically significant expression of several intracellular antiviral genes was noted, which may limit viral load but fails to stop replication. EBOV gene expression profiling is of vital importance in understanding pathogenesis and devising novel therapeutic treatments such as small-molecule inhibitors.

A Network Approach of Gene Co-expression in the Zea mays/Aspergillus flavus Pathosystem to Map Host/Pathogen Interaction Pathways

OpenAIRE

Musungu, Bryan M.; Bhatnagar, Deepak; Brown, Robert L.; Payne, Gary A.; OBrian, Greg; Fakhoury, Ahmad M.; Geisler, Matt

2016-01-01

A gene co-expression network (GEN) was generated using a dual RNA-seq study with the fungal pathogen Aspergillus flavus and its plant host Zea mays during the initial 3 days of infection. The analysis deciphered novel pathways and mapped genes of interest in both organisms during the infection. This network revealed a high degree of connectivity in many of the previously recognized pathways in Z. mays such as jasmonic acid, ethylene, and reactive oxygen species (ROS). For the pathogen A. flav...

Assessing pathogenicity of MLH1 variants by co-expression of human MLH1 and PMS2 genes in yeast

Energy Technology Data Exchange (ETDEWEB)

Vogelsang, Matjaz; Comino, Aleksandra; Zupanec, Neja [Department for Biosynthesis and Biotransformation, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana (Slovenia); Hudler, Petra [Medical Center for Molecular Biology, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana (Slovenia); Komel, Radovan [Department for Biosynthesis and Biotransformation, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana (Slovenia); Medical Center for Molecular Biology, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana (Slovenia)

2009-10-28

Loss of DNA mismatch repair (MMR) in humans, mainly due to mutations in the hMLH1 gene, is linked to hereditary nonpolyposis colorectal cancer (HNPCC). Because not all MLH1 alterations result in loss of MMR function, accurate characterization of variants and their classification in terms of their effect on MMR function is essential for reliable genetic testing and effective treatment. To date, in vivo assays for functional characterization of MLH1 mutations performed in various model systems have used episomal expression of the modified MMR genes. We describe here a novel approach to determine accurately the functional significance of hMLH1 mutations in vivo, based on co-expression of human MLH1 and PMS2 in yeast cells. Yeast MLH1 and PMS1 genes, whose protein products form the MutLα complex, were replaced by human orthologs directly on yeast chromosomes by homologous recombination, and the resulting MMR activity was tested. The yeast strain co-expressing hMLH1 and hPMS2 exhibited the same mutation rate as the wild-type. Eight cancer-related MLH1 variants were introduced, using the same approach, into the prepared yeast model, and their effect on MMR function was determined. Five variants (A92P, S93G, I219V, K618R and K618T) were classified as non-pathogenic, whereas variants T117M, Y646C and R659Q were characterized as pathogenic. Results of our in vivo yeast-based approach correlate well with clinical data in five out of seven hMLH1 variants and the described model was thus shown to be useful for functional characterization of MLH1 variants in cancer patients found throughout the entire coding region of the gene.

Assessing pathogenicity of MLH1 variants by co-expression of human MLH1 and PMS2 genes in yeast

Directory of Open Access Journals (Sweden)

Hudler Petra

2009-10-01

Full Text Available Abstract Background Loss of DNA mismatch repair (MMR in humans, mainly due to mutations in the hMLH1 gene, is linked to hereditary nonpolyposis colorectal cancer (HNPCC. Because not all MLH1 alterations result in loss of MMR function, accurate characterization of variants and their classification in terms of their effect on MMR function is essential for reliable genetic testing and effective treatment. To date, in vivo assays for functional characterization of MLH1 mutations performed in various model systems have used episomal expression of the modified MMR genes. We describe here a novel approach to determine accurately the functional significance of hMLH1 mutations in vivo, based on co-expression of human MLH1 and PMS2 in yeast cells. Methods Yeast MLH1 and PMS1 genes, whose protein products form the MutLα complex, were replaced by human orthologs directly on yeast chromosomes by homologous recombination, and the resulting MMR activity was tested. Results The yeast strain co-expressing hMLH1 and hPMS2 exhibited the same mutation rate as the wild-type. Eight cancer-related MLH1 variants were introduced, using the same approach, into the prepared yeast model, and their effect on MMR function was determined. Five variants (A92P, S93G, I219V, K618R and K618T were classified as non-pathogenic, whereas variants T117M, Y646C and R659Q were characterized as pathogenic. Conclusion Results of our in vivo yeast-based approach correlate well with clinical data in five out of seven hMLH1 variants and the described model was thus shown to be useful for functional characterization of MLH1 variants in cancer patients found throughout the entire coding region of the gene.

Assessing pathogenicity of MLH1 variants by co-expression of human MLH1 and PMS2 genes in yeast

International Nuclear Information System (INIS)

Vogelsang, Matjaz; Comino, Aleksandra; Zupanec, Neja; Hudler, Petra; Komel, Radovan

2009-01-01

Loss of DNA mismatch repair (MMR) in humans, mainly due to mutations in the hMLH1 gene, is linked to hereditary nonpolyposis colorectal cancer (HNPCC). Because not all MLH1 alterations result in loss of MMR function, accurate characterization of variants and their classification in terms of their effect on MMR function is essential for reliable genetic testing and effective treatment. To date, in vivo assays for functional characterization of MLH1 mutations performed in various model systems have used episomal expression of the modified MMR genes. We describe here a novel approach to determine accurately the functional significance of hMLH1 mutations in vivo, based on co-expression of human MLH1 and PMS2 in yeast cells. Yeast MLH1 and PMS1 genes, whose protein products form the MutLα complex, were replaced by human orthologs directly on yeast chromosomes by homologous recombination, and the resulting MMR activity was tested. The yeast strain co-expressing hMLH1 and hPMS2 exhibited the same mutation rate as the wild-type. Eight cancer-related MLH1 variants were introduced, using the same approach, into the prepared yeast model, and their effect on MMR function was determined. Five variants (A92P, S93G, I219V, K618R and K618T) were classified as non-pathogenic, whereas variants T117M, Y646C and R659Q were characterized as pathogenic. Results of our in vivo yeast-based approach correlate well with clinical data in five out of seven hMLH1 variants and the described model was thus shown to be useful for functional characterization of MLH1 variants in cancer patients found throughout the entire coding region of the gene

Development of feed supplementation strategies for improving the productivity of dairy cattle on smallholder farms in Africa. Proceedings of the final research co-ordination meeting of a co-ordinated research project

Energy Technology Data Exchange (ETDEWEB)

NONE

1999-07-01

The Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture through co-ordinated research projects (CRP) supports studies aimed at improving livestock productivity in developing countries through the application of nuclear and related techniques. These studies have focused on animal nutrition, animal reproduction and more recently on animal nutrition/reproduction interactions with emphasis on smallholder farming systems. The primary aim of this CRP was to identify approaches for improving the productivity of dairy cattle maintained on smallholder farms in peri-urban areas. Central to the approach was to first obtain baseline information on productivity and reproductive efficiency and thereby identify nutritional and management constraints. Subsequently, corrective measures were developed and tested, keeping in mind the need for maximising the efficiency of current production systems and sustaining the nutrient supply through practical and economically feasible feed supplementation strategies developed using locally available feed resources. In addition the project envisaged contributing to enhancing the level of expertise within the national animal production research institutes in the region, to encourage close contact and interaction between scientists and institutions in Africa and to promote scientific information exchange on a regional basis. Through the project substantial progress was made in understanding the relationship between nutrient supply and productive and reproductive functions in dairy cattle on smallholder farming systems. Most of the participating countries were able to develop and test cost-effective feed supplementation strategies which improved both milk production and/or reproductive efficiency. The present publication contains the reports from participants of the project presented at the final Research Co-ordination Meeting held in Vienna from 7 to 11 September 1998 Refs, figs, tabs

Development of feed supplementation strategies for improving the productivity of dairy cattle on smallholder farms in Africa. Proceedings of the final research co-ordination meeting of a co-ordinated research project

International Nuclear Information System (INIS)

1999-07-01

The Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture through co-ordinated research projects (CRP) supports studies aimed at improving livestock productivity in developing countries through the application of nuclear and related techniques. These studies have focused on animal nutrition, animal reproduction and more recently on animal nutrition/reproduction interactions with emphasis on smallholder farming systems. The primary aim of this CRP was to identify approaches for improving the productivity of dairy cattle maintained on smallholder farms in peri-urban areas. Central to the approach was to first obtain baseline information on productivity and reproductive efficiency and thereby identify nutritional and management constraints. Subsequently, corrective measures were developed and tested, keeping in mind the need for maximising the efficiency of current production systems and sustaining the nutrient supply through practical and economically feasible feed supplementation strategies developed using locally available feed resources. In addition the project envisaged contributing to enhancing the level of expertise within the national animal production research institutes in the region, to encourage close contact and interaction between scientists and institutions in Africa and to promote scientific information exchange on a regional basis. Through the project substantial progress was made in understanding the relationship between nutrient supply and productive and reproductive functions in dairy cattle on smallholder farming systems. Most of the participating countries were able to develop and test cost-effective feed supplementation strategies which improved both milk production and/or reproductive efficiency. The present publication contains the reports from participants of the project presented at the final Research Co-ordination Meeting held in Vienna from 7 to 11 September 1998

Transient expression of β-glucuronidase gene in indica and ...

African Journals Online (AJOL)

Owner

co-transfer of DNAs to cells was monitored by analyzing transient gus expression 24 h after .... induction frequency was determined by measuring the ... Effect of age on transient expression of gus gene and production of hygromycin .... japonica varieties via electric discharge particle acceleration of .... yellow stem borer.

Co-expression of an Erwinia chrysanthemi pectate lyase-encoding gene (pelE) and an E. carotovora polygalacturonase-encoding gene (peh1) in Saccharomyces cerevisiae.

Science.gov (United States)

Laing, E; Pretorius, I S

1993-05-01

A pectate lyase (PL)-encoding gene (pelE) from Erwinia chrysanthemi and a polygalacturonase (PG)-encoding gene (peh1) from E. carotovora were each inserted between a novel yeast expression-secretion cassette and a yeast gene terminator, and cloned separately into a yeast-centromeric shuttle vector (YCp50), generating recombinant plasmids pAMS12 and pAMS13. Transcription initiation signals present in the expression-secretion cassette were derived from the yeast alcohol dehydrogenase gene promoter (ADC1P), whereas the transcription termination signals were derived from the yeast tryptophan synthase gene terminator (TRP5T). Secretion of PL and PG was directed by the signal sequence of the yeast mating pheromone alpha-factor (MF alpha 1s). A pectinase cassette comprising ADC1P-MF alpha 1s-pelE-TRP5T and ADC1P-MF alpha 1s-peh1-TRP5T was subcloned into YCp50, generating plasmid pAMS14. Subsequently, the dominant selectable Geneticin G418-resistance (GtR) marker, APH1, inserted between the yeast uridine diphosphoglucose 4-epimerase gene promoter (GAL10P) and yeast orotidine-5'-phosphate carboxylase gene terminator (URA3T), was cloned into pAMS14, resulting in plasmid pAMS15. Plasmids pAMS12, pAMS13 and pAMS14 were transformed into a laboratory strain of Saccharomyces cerevisiae, whereas pAMS15 was stably introduced into two commercial wine yeast strains. DNA-DNA and DNA-RNA hybridization analyses revealed the presence of these plasmids, and the pelE and peh1 transcripts in the yeast transformants, respectively. A polypectate agarose assay indicated the extracellular production of biologically active PL and PG by the S. cerevisiae transformants and confirmed that co-expression of the pelE and peh1 genes synergistically enhanced pectate degradation.

Neutralization of Bacterial YoeBSpn Toxicity and Enhanced Plant Growth in Arabidopsis thaliana via Co-Expression of the Toxin-Antitoxin Genes

Science.gov (United States)

Abu Bakar, Fauziah; Yeo, Chew Chieng; Harikrishna, Jennifer Ann

2016-01-01

Bacterial toxin-antitoxin (TA) systems have various cellular functions, including as part of the general stress response. The genome of the Gram-positive human pathogen Streptococcus pneumoniae harbors several putative TA systems, including yefM-yoeBSpn, which is one of four systems that had been demonstrated to be biologically functional. Overexpression of the yoeBSpn toxin gene resulted in cell stasis and eventually cell death in its native host, as well as in Escherichia coli. Our previous work showed that induced expression of a yoeBSpn toxin-Green Fluorescent Protein (GFP) fusion gene apparently triggered apoptosis and was lethal in the model plant, Arabidopsis thaliana. In this study, we investigated the effects of co-expression of the yefMSpn antitoxin and yoeBSpn toxin-GFP fusion in transgenic A. thaliana. When co-expressed in Arabidopsis, the YefMSpn antitoxin was found to neutralize the toxicity of YoeBSpn-GFP. Interestingly, the inducible expression of both yefMSpn antitoxin and yoeBSpn toxin-GFP fusion in transgenic hybrid Arabidopsis resulted in larger rosette leaves and taller plants with a higher number of inflorescence stems and increased silique production. To our knowledge, this is the first demonstration of a prokaryotic antitoxin neutralizing its cognate toxin in plant cells. PMID:27104531

Neutralization of Bacterial YoeBSpn Toxicity and Enhanced Plant Growth in Arabidopsis thaliana via Co-Expression of the Toxin-Antitoxin Genes

Directory of Open Access Journals (Sweden)

Fauziah Abu Bakar

2016-04-01

Full Text Available Bacterial toxin-antitoxin (TA systems have various cellular functions, including as part of the general stress response. The genome of the Gram-positive human pathogen Streptococcus pneumoniae harbors several putative TA systems, including yefM-yoeBSpn, which is one of four systems that had been demonstrated to be biologically functional. Overexpression of the yoeBSpn toxin gene resulted in cell stasis and eventually cell death in its native host, as well as in Escherichia coli. Our previous work showed that induced expression of a yoeBSpn toxin-Green Fluorescent Protein (GFP fusion gene apparently triggered apoptosis and was lethal in the model plant, Arabidopsis thaliana. In this study, we investigated the effects of co-expression of the yefMSpn antitoxin and yoeBSpn toxin-GFP fusion in transgenic A. thaliana. When co-expressed in Arabidopsis, the YefMSpn antitoxin was found to neutralize the toxicity of YoeBSpn-GFP. Interestingly, the inducible expression of both yefMSpn antitoxin and yoeBSpn toxin-GFP fusion in transgenic hybrid Arabidopsis resulted in larger rosette leaves and taller plants with a higher number of inflorescence stems and increased silique production. To our knowledge, this is the first demonstration of a prokaryotic antitoxin neutralizing its cognate toxin in plant cells.

Neighboring Genes Show Correlated Evolution in Gene Expression

Science.gov (United States)

Ghanbarian, Avazeh T.; Hurst, Laurence D.

2015-01-01

When considering the evolution of a gene’s expression profile, we commonly assume that this is unaffected by its genomic neighborhood. This is, however, in contrast to what we know about the lack of autonomy between neighboring genes in gene expression profiles in extant taxa. Indeed, in all eukaryotic genomes genes of similar expression-profile tend to cluster, reflecting chromatin level dynamics. Does it follow that if a gene increases expression in a particular lineage then the genomic neighbors will also increase in their expression or is gene expression evolution autonomous? To address this here we consider evolution of human gene expression since the human-chimp common ancestor, allowing for both variation in estimation of current expression level and error in Bayesian estimation of the ancestral state. We find that in all tissues and both sexes, the change in gene expression of a focal gene on average predicts the change in gene expression of neighbors. The effect is highly pronounced in the immediate vicinity (genes increasing their expression in humans tend to avoid nuclear lamina domains and be enriched for the gene activator 5-hydroxymethylcytosine, we conclude that, most probably owing to chromatin level control of gene expression, a change in gene expression of one gene likely affects the expression evolution of neighbors, what we term expression piggybacking, an analog of hitchhiking. PMID:25743543

In vitro techniques for selection of radiation induced mutations adapted to adverse environmental conditions. Proceedings of a final research co-ordination meeting

International Nuclear Information System (INIS)

2001-06-01

The ever increasing human population and dwindling land and water resources worldwide make it essential to produce more food, fibre and fodder from less and less land. During the last century, plant breeding contributed remarkably to increasing food by producing varieties which give higher yield, have improved quality and nutrition, and resist diseases and pests. Nearly 50% of the increase in food production in Asia during the last fifty years can be attributed to the high yielding, short height varieties of rice and wheat, the remaining to the improved agronomic inputs and management. Many crops, such as cassava, potato, pineapple, sweet potato, sugarcane, banana and plantain are major food crops, and others such as sugarcane and pineapple are important to the economies of many developing countries. One of the solutions to have a sustainable and secure food production is to breed varieties which are tolerant of stress conditions during their growth and development. Hence a Co-ordinated Research Project on In vitro Techniques for Selection of Radiation Induced Mutations Adapted to Adverse Environmental Conditions was initiated and focused primarily on the improvement of vegetatively propagated plants. Since the inception of this project, several participating scientists established the optimal dose requirement for in vitro cultured material. Investigations were carried out on the effect of radiation to alter traits which affect survival under stress conditions and high temperature stress in potato, pineapple, sweet potato and garlic. The possibility to change traits such as tolerance to saline and water logged soils in sugarcane and gene regulation for salinity tolerance were studied. The limited number of available reports suggest that callus cultures are much more sensitive to radiation treatment and require much lower doses (2 to 5 Gy) than stem cuttings or seeds, and that relatively higher doses (15 to 20 Gy) cause necrosis or loss of regenerative capacity. The

In vitro techniques for selection of radiation induced mutations adapted to adverse environmental conditions. Proceedings of a final research co-ordination meeting

Energy Technology Data Exchange (ETDEWEB)

NONE

2001-06-01

The ever increasing human population and dwindling land and water resources worldwide make it essential to produce more food, fibre and fodder from less and less land. During the last century, plant breeding contributed remarkably to increasing food by producing varieties which give higher yield, have improved quality and nutrition, and resist diseases and pests. Nearly 50% of the increase in food production in Asia during the last fifty years can be attributed to the high yielding, short height varieties of rice and wheat, the remaining to the improved agronomic inputs and management. Many crops, such as cassava, potato, pineapple, sweet potato, sugarcane, banana and plantain are major food crops, and others such as sugarcane and pineapple are important to the economies of many developing countries. One of the solutions to have a sustainable and secure food production is to breed varieties which are tolerant of stress conditions during their growth and development. Hence a Co-ordinated Research Project on In vitro Techniques for Selection of Radiation Induced Mutations Adapted to Adverse Environmental Conditions was initiated and focused primarily on the improvement of vegetatively propagated plants. Since the inception of this project, several participating scientists established the optimal dose requirement for in vitro cultured material. Investigations were carried out on the effect of radiation to alter traits which affect survival under stress conditions and high temperature stress in potato, pineapple, sweet potato and garlic. The possibility to change traits such as tolerance to saline and water logged soils in sugarcane and gene regulation for salinity tolerance were studied. The limited number of available reports suggest that callus cultures are much more sensitive to radiation treatment and require much lower doses (2 to 5 Gy) than stem cuttings or seeds, and that relatively higher doses (15 to 20 Gy) cause necrosis or loss of regenerative capacity. The

Gene Expression Commons: an open platform for absolute gene expression profiling.

Directory of Open Access Journals (Sweden)

Jun Seita

Full Text Available Gene expression profiling using microarrays has been limited to comparisons of gene expression between small numbers of samples within individual experiments. However, the unknown and variable sensitivities of each probeset have rendered the absolute expression of any given gene nearly impossible to estimate. We have overcome this limitation by using a very large number (>10,000 of varied microarray data as a common reference, so that statistical attributes of each probeset, such as the dynamic range and threshold between low and high expression, can be reliably discovered through meta-analysis. This strategy is implemented in a web-based platform named "Gene Expression Commons" (https://gexc.stanford.edu/ which contains data of 39 distinct highly purified mouse hematopoietic stem/progenitor/differentiated cell populations covering almost the entire hematopoietic system. Since the Gene Expression Commons is designed as an open platform, investigators can explore the expression level of any gene, search by expression patterns of interest, submit their own microarray data, and design their own working models representing biological relationship among samples.

Interplay of Noisy Gene Expression and Dynamics Explains Patterns of Bacterial Operon Organization

Science.gov (United States)

Igoshin, Oleg

2011-03-01

Bacterial chromosomes are organized into operons -- sets of genes co-transcribed into polycistronic messenger RNA. Hypotheses explaining the emergence and maintenance of operons include proportional co-regulation, horizontal transfer of intact ``selfish'' operons, emergence via gene duplication, and co-production of physically interacting proteins to speed their association. We hypothesized an alternative: operons can reduce or increase intrinsic gene expression noise in a manner dependent on the post-translational interactions, thereby resulting in selection for or against operons in depending on the network architecture. We devised five classes of two-gene network modules and show that the effects of operons on intrinsic noise depend on class membership. Two classes exhibit decreased noise with co-transcription, two others reveal increased noise, and the remaining one does not show a significant difference. To test our modeling predictions we employed bioinformatic analysis to determine the relationship gene expression noise and operon organization. The results confirm the overrepresentation of noise-minimizing operon architectures and provide evidence against other hypotheses. Our results thereby suggest a central role for gene expression noise in selecting for or maintaining operons in bacterial chromosomes. This demonstrates how post-translational network dynamics may provide selective pressure for organizing bacterial chromosomes, and has practical consequences for designing synthetic gene networks. This work is supported by National Institutes of Health grant 1R01GM096189-01.

Regulation of gene expression by photosynthetic signals triggered through modified CO2 availability

Directory of Open Access Journals (Sweden)

Wormuth Dennis

2006-08-01

Full Text Available Abstract Background To coordinate metabolite fluxes and energy availability, plants adjust metabolism and gene expression to environmental changes through employment of interacting signalling pathways. Results Comparing the response of Arabidopsis wild-type plants with that of the mutants adg1, pgr1 and vtc1 upon altered CO2-availability, the regulatory role of the cellular energy status, photosynthetic electron transport, the redox state and concentration of ascorbate and glutathione and the assimilatory force was analyzed in relation to the transcript abundance of stress-responsive nuclear encoded genes and psaA and psbA encoding the reaction centre proteins of photosystem I and II, respectively. Transcript abundance of Bap1, Stp1, psaA and psaB was coupled with seven metabolic parameters. Especially for psaA and psaB, the complex analysis demonstrated that the assumed PQ-dependent redox control is subordinate to signals linked to the relative availability of 3-PGA and DHAP, which define the assimilatory force. For the transcripts of sAPx and Csd2 high correlations with the calculated redox state of NADPH were observed in pgr1, but not in wild-type, suggesting that in wild-type plants signals depending on thylakoid acidification overlay a predominant redox-signal. Strongest correlation with the redox state of ascorbate was observed for 2CPA, whose transcript abundance regulation however was almost insensitive to the ascorbate content demonstrating dominance of redox regulation over metabolite sensing. Conclusion In the mutants, signalling pathways are partially uncoupled, demonstrating dominance of metabolic control of photoreaction centre expression over sensing the redox state of the PQ-pool. The balance between the cellular redox poise and the energy signature regulates sAPx and Csd2 transcript abundance, while 2CPA expression is primarily redox-controlled.

Importance of correlation between gene expression levels: application to the type I interferon signature in rheumatoid arthritis.

Science.gov (United States)

Reynier, Frédéric; Petit, Fabien; Paye, Malick; Turrel-Davin, Fanny; Imbert, Pierre-Emmanuel; Hot, Arnaud; Mougin, Bruno; Miossec, Pierre

2011-01-01

The analysis of gene expression data shows that many genes display similarity in their expression profiles suggesting some co-regulation. Here, we investigated the co-expression patterns in gene expression data and proposed a correlation-based research method to stratify individuals. Using blood from rheumatoid arthritis (RA) patients, we investigated the gene expression profiles from whole blood using Affymetrix microarray technology. Co-expressed genes were analyzed by a biclustering method, followed by gene ontology analysis of the relevant biclusters. Taking the type I interferon (IFN) pathway as an example, a classification algorithm was developed from the 102 RA patients and extended to 10 systemic lupus erythematosus (SLE) patients and 100 healthy volunteers to further characterize individuals. We developed a correlation-based algorithm referred to as Classification Algorithm Based on a Biological Signature (CABS), an alternative to other approaches focused specifically on the expression levels. This algorithm applied to the expression of 35 IFN-related genes showed that the IFN signature presented a heterogeneous expression between RA, SLE and healthy controls which could reflect the level of global IFN signature activation. Moreover, the monitoring of the IFN-related genes during the anti-TNF treatment identified changes in type I IFN gene activity induced in RA patients. In conclusion, we have proposed an original method to analyze genes sharing an expression pattern and a biological function showing that the activation levels of a biological signature could be characterized by its overall state of correlation.

Use of isotopic tracers in studies of herbicides performance on grasses and sedges. Report of a final research co-ordination meeting

Energy Technology Data Exchange (ETDEWEB)

NONE

1998-02-01

Herbicide products as sold to the user are a mixture or formulation of active ingredient, surfactants and other adjuvants, plus a carrier, which will be a liquid if the formulation is to be applied as a spray. The adjuvants affect the characteristics of the spray, including the retention of the droplets by plant surfaces and the penetration of active ingredient into the plant. Thus they play a critical part in determining the phototoxicity and selectivity of the product. The IAEA organized a co-ordinated research programme in 1992 to explore the possibility of improving the performance of the herbicide glyphosate on Cyperus rotundus (purple nutsedge), commonly regarded as the ``world`s worst weed``, by modifying the commercial formulation using penetration studies with {sup 14}C labelled glyphosate as the initial screening procedure. This TECDOC summarizes the outcome of the programme and includes the papers presented at the research co-ordination meeting held in Los Banos, Philippines, 17-21 February 1997. The co-operation of the Monsanto Company, the manufacturer of the glyphosate herbicide, is gratefully acknowledged. Refs, figs, tabs.

Use of isotopic tracers in studies of herbicides performance on grasses and sedges. Report of a final research co-ordination meeting

International Nuclear Information System (INIS)

1998-02-01

Herbicide products as sold to the user are a mixture or formulation of active ingredient, surfactants and other adjuvants, plus a carrier, which will be a liquid if the formulation is to be applied as a spray. The adjuvants affect the characteristics of the spray, including the retention of the droplets by plant surfaces and the penetration of active ingredient into the plant. Thus they play a critical part in determining the phototoxicity and selectivity of the product. The IAEA organized a co-ordinated research programme in 1992 to explore the possibility of improving the performance of the herbicide glyphosate on Cyperus rotundus (purple nutsedge), commonly regarded as the ''world's worst weed'', by modifying the commercial formulation using penetration studies with 14 C labelled glyphosate as the initial screening procedure. This TECDOC summarizes the outcome of the programme and includes the papers presented at the research co-ordination meeting held in Los Banos, Philippines, 17-21 February 1997. The co-operation of the Monsanto Company, the manufacturer of the glyphosate herbicide, is gratefully acknowledged

Dopamine in the Auditory Brainstem and Midbrain: Co-localization with Amino Acid Neurotransmitters and Gene Expression following Cochlear Trauma

Directory of Open Access Journals (Sweden)

Avril Genene eHolt

2015-07-01

Full Text Available Dopamine (DA modulates the effects of amino acid neurotransmitters, including GABA and glutamate, in motor, visual, olfactory and reward systems (Hnasko et al., 2010; Stuber et al., 2010; Hnasko and Edwards, 2012. The results suggest that DA may play a similar modulatory role in the auditory pathways. Previous studies have shown that deafness results in decreased GABA release, changes in excitatory neurotransmitter levels, and increased spontaneous neuronal activity within brainstem regions related to auditory function. Modulation of the expression and localization of tyrosine hydroxylase (TH; the rate limiting enzyme in the production of DA in the IC following cochlear trauma has been previously reported (Tong et al., 2005. In the current study the possibility of co-localization of TH with amino acid neurotransmitters (AANs was examined. Changes in the gene expression of TH were compared with changes in the gene expression of markers for AANs in the cochlear nucleus (CN and IC to determine whether those deafness related changes occur concurrently. The results indicate that bilateral cochlear ablation significantly reduced TH gene expression in the CN after two months while in the IC the reduction in TH was observed at both three days and two months following ablation. Furthermore, in the CN, glycine transporter 2 (GlyT2 and the GABA transporter (GABAtp were also significantly reduced only after two months. However, in the IC, DA receptor 1 (DRDA1, vesicular glutamate transporters 2 and 3 (vGluT2, vGluT3, GABAtp and GAD67 were reduced in expression both at the three day and two month time points. A close relationship between the distribution of TH and several of the AANs was determined in both the CN and the IC. In addition, GlyT2 and vGluT3 each co-localized with TH within IC somata and dendrites. Therefore, the results of the current study suggest that DA is spatially well positioned to influence the effects of AANs on auditory neurons.

Co-ordinated research programme on the use of nuclear and nuclear-related techniques in the study of environmental pollution associated with solid wastes

International Nuclear Information System (INIS)

1991-01-01

A co-ordinated research programme on the use of nuclear and nuclear-related techniques in the study of environmental pollution associated with solid wastes was started by the IAEA in December 1987 and now comprises twenty-three participants from twenty-one countries. Topics of interest in this programme include studies of atmospheric aerosols, coal fly ash, incinerator ash, sewage sludge and a variety of other environmental specimens contaminated with solid wastes. The analytical techniques used include neutron activation analysis, particle-induced X-ray emission and energy-dispersive X-ray fluorescence. This report summarizes the discussions that took place during the second research co-ordination meeting. Working papers presented by the participants are included as annexes and have been indexed separately. Refs, figs and tabs

Co-ordinated research programme on the use of nuclear and nuclear-related techniques in the study of environmental pollution associated with solid wastes

International Nuclear Information System (INIS)

1992-01-01

A co-ordinated research programme on the use of nuclear and nuclear-related techniques in the study of environmental pollution associated with solid wastes was started by the IAEA in December 1987 and now comprises nineteen participants from seventeen countries. Topics of interest in this programme include studies of atmospheric aerosols, coal fly ash, incinerator ash, sewage sludge and a variety of other environmental specimens contaminated with solid wastes. The analytical techniques used include neutron activation analysis, particle-induced X-ray emission and energy-dispersive X-ray fluorescence. This report summarizes the discussions that took place during the third research co-ordination meeting. Working papers presented by the participants are included as annexes and have been indexed separately. Refs, figs and tabs

Drosophila Myc is required for normal DREF gene expression

International Nuclear Information System (INIS)

Dang Thi Phuong Thao; Seto, Hirokazu; Yamaguchi, Masamitsu

2008-01-01

The Drosophila DNA replication-related element-binding factor (dDREF) is required for the expression of many proliferation-related genes carrying the DRE sequence, 5'-TATCGATA. Finding a canonical E-box, 5'-CACGTG, in the dDREF gene promoter prompted us to explore the possibility that the dDREF gene is a target of Drosophila Myc (dMyc). Luciferase transient expression assays combined with RNA interference in Drosophila S2 cells revealed that knockdown of dmyc reduced dDREF gene promoter activity by 35% to 82%, an effect at least partly mediated by the E-box in the promoter. dm 4 /Y hemizygous mutant larvae demonstrated no maternal dMyc and severe impairment of dDREF mRNA transcription. dMyc loss of function in dm 2 /dm 2 homozygous mutant follicle cell clones also resulted in loss of anti-dDREF immunostaining in nuclei. In contrast, co-expression of dMyc-dMax up-regulated dDREF promoter activity in S2 cells. Furthermore, dMyc over-expressing clones exhibited a high level of dDREF gene expression in wing and eye discs. These results taken together indicate that dMyc is indeed required for dDREF gene expression

Application of Weighted Gene Co-expression Network Analysis for Data from Paired Design.

Science.gov (United States)

Li, Jianqiang; Zhou, Doudou; Qiu, Weiliang; Shi, Yuliang; Yang, Ji-Jiang; Chen, Shi; Wang, Qing; Pan, Hui

2018-01-12

Investigating how genes jointly affect complex human diseases is important, yet challenging. The network approach (e.g., weighted gene co-expression network analysis (WGCNA)) is a powerful tool. However, genomic data usually contain substantial batch effects, which could mask true genomic signals. Paired design is a powerful tool that can reduce batch effects. However, it is currently unclear how to appropriately apply WGCNA to genomic data from paired design. In this paper, we modified the current WGCNA pipeline to analyse high-throughput genomic data from paired design. We illustrated the modified WGCNA pipeline by analysing the miRNA dataset provided by Shiah et al. (2014), which contains forty oral squamous cell carcinoma (OSCC) specimens and their matched non-tumourous epithelial counterparts. OSCC is the sixth most common cancer worldwide. The modified WGCNA pipeline identified two sets of novel miRNAs associated with OSCC, in addition to the existing miRNAs reported by Shiah et al. (2014). Thus, this work will be of great interest to readers of various scientific disciplines, in particular, genetic and genomic scientists as well as medical scientists working on cancer.

MeSH key terms for validation and annotation of gene expression clusters

Energy Technology Data Exchange (ETDEWEB)

Rechtsteiner, A. (Andreas); Rocha, L. M. (Luis Mateus)

2004-01-01

Integration of different sources of information is a great challenge for the analysis of gene expression data, and for the field of Functional Genomics in general. As the availability of numerical data from high-throughput methods increases, so does the need for technologies that assist in the validation and evaluation of the biological significance of results extracted from these data. In mRNA assaying with microarrays, for example, numerical analysis often attempts to identify clusters of co-expressed genes. The important task to find the biological significance of the results and validate them has so far mostly fallen to the biological expert who had to perform this task manually. One of the most promising avenues to develop automated and integrative technology for such tasks lies in the application of modern Information Retrieval (IR) and Knowledge Management (KM) algorithms to databases with biomedical publications and data. Examples of databases available for the field are bibliographic databases c ntaining scientific publications (e.g. MEDLINE/PUBMED), databases containing sequence data (e.g. GenBank) and databases of semantic annotations (e.g. the Gene Ontology Consortium and Medical Subject Headings (MeSH)). We present here an approach that uses the MeSH terms and their concept hierarchies to validate and obtain functional information for gene expression clusters. The controlled and hierarchical MeSH vocabulary is used by the National Library of Medicine (NLM) to index all the articles cited in MEDLINE. Such indexing with a controlled vocabulary eliminates some of the ambiguity due to polysemy (terms that have multiple meanings) and synonymy (multiple terms have similar meaning) that would be encountered if terms would be extracted directly from the articles due to differing article contexts or author preferences and background. Further, the hierarchical organization of the MeSH terms can illustrate the conceptuallfunctional relationships of genes

An extensive (co-expression analysis tool for the cytochrome P450 superfamily in Arabidopsis thaliana

Directory of Open Access Journals (Sweden)

Provart Nicholas J

2008-04-01

Full Text Available Abstract Background Sequencing of the first plant genomes has revealed that cytochromes P450 have evolved to become the largest family of enzymes in secondary metabolism. The proportion of P450 enzymes with characterized biochemical function(s is however very small. If P450 diversification mirrors evolution of chemical diversity, this points to an unexpectedly poor understanding of plant metabolism. We assumed that extensive analysis of gene expression might guide towards the function of P450 enzymes, and highlight overlooked aspects of plant metabolism. Results We have created a comprehensive database, 'CYPedia', describing P450 gene expression in four data sets: organs and tissues, stress response, hormone response, and mutants of Arabidopsis thaliana, based on public Affymetrix ATH1 microarray expression data. P450 expression was then combined with the expression of 4,130 re-annotated genes, predicted to act in plant metabolism, for co-expression analyses. Based on the annotation of co-expressed genes from diverse pathway annotation databases, co-expressed pathways were identified. Predictions were validated for most P450s with known functions. As examples, co-expression results for P450s related to plastidial functions/photosynthesis, and to phenylpropanoid, triterpenoid and jasmonate metabolism are highlighted here. Conclusion The large scale hypothesis generation tools presented here provide leads to new pathways, unexpected functions, and regulatory networks for many P450s in plant metabolism. These can now be exploited by the community to validate the proposed functions experimentally using reverse genetics, biochemistry, and metabolic profiling.

Glycoprotein is enough for sindbis virus-derived DNA vector to express heterogenous genes

Directory of Open Access Journals (Sweden)

Fu Juanjuan

2011-07-01

Full Text Available Abstract To investigate the necessity and potential application of structural genes for expressing heterogenous genes from Sindbis virus-derived vector, the DNA-based expression vector pVaXJ was constructed by placing the recombinant genome of sindbis-like virus XJ-160 under the control of the human cytomegalovirus (CMV promoter of the plasmid pVAX1, in which viral structural genes were replaced by a polylinker cassette to allow for insertion of heterologous genes. The defect helper plasmids pVaE or pVaC were developed by cloning the gene of glycoprotein E3E26KE1 or capsid protein of XJ-160 virus into pVAX1, respectively. The report gene cassette pVaXJ-EGFP or pV-Gluc expressing enhanced green fluorescence protein (EGFP or Gaussia luciferase (G.luc were constructed by cloning EGFP or G.luc gene into pVaXJ. EGFP or G.luc was expressed in the BHK-21 cells co-transfected with report gene cassettes and pVaE at levels that were comparable to those produced by report gene cassettes, pVaC and pVaE and were much higher than the levels produced by report gene cassette and pVaC, suggesting that glycoprotein is enough for Sindbis virus-derived DNA vector to express heterogenous genes in host cells. The method of gene expression from Sindbis virus-based DNA vector only co-transfected with envelop E gene increase the conveniency and the utility of alphavirus-based vector systems in general.

Optimizing nitrogen fertilizer application to irrigated wheat. Results of a co-ordinated research project. 1994-1998

International Nuclear Information System (INIS)

2000-07-01

This TECDOC summarizes the results of a Co-ordinated Research Project (CRP) on the Use of Nuclear Techniques for Optimizing Fertilizer Application under Irrigated Wheat to Increase the Efficient Use of Nitrogen Fertilizer and Consequently Reduce Environmental Pollution. The project was carried out between 1994 and 1998 through the technical co-ordination of the Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture. Fourteen Member States of the IAEA and FAO carried out a series of field experiments aimed at improving irrigation water and fertilizer-N uptake efficiencies through integrated management of the complex Interactions involving inputs, soils, climate, and wheat cultivars. Its goals were: to investigate various aspects of fertilizer N uptake efficiency of wheat crops under irrigation through an interregional research network involving countries growing large areas of irrigated wheat; to use 15 N and the soil-moisture neutron probe to determine the fate of applied N, to follow water and nitrate movement in the soil, and to determine water balance and water-use efficiency in irrigated wheat cropping systems; to use the data generated to further develop and refine various relationships in the Ceres-Wheat computer simulation model; to use the knowledge generated to produce a N-rate-recommendation package to refine specific management strategies with respect to fertilizer applications and expected yields

Nine co-localized cytochrome P450 genes of the CYP2N, CYP2AD, and CYP2P gene families in the mangrove killifish Kryptolebias marmoratus genome: Identification and expression in response to B[α]P, BPA, OP, and NP.

Science.gov (United States)

Puthumana, Jayesh; Kim, Bo-Mi; Jeong, Chang-Bum; Kim, Duck-Hyun; Kang, Hye-Min; Jung, Jee-Hyun; Kim, Il-Chan; Hwang, Un-Ki; Lee, Jae-Seong

2017-06-01

The CYP2 genes are the largest and most diverse cytochrome P450 (CYP) subfamily in vertebrates. We have identified nine co-localized CYP2 genes (∼55kb) in a new cluster in the genome of the highly resilient ecotoxicological fish model Kryptolebias marmoratus. Molecular characterization, temporal and tissue-specific expression pattern, and response to xenobiotics of these genes were examined. The CYP2 gene clusters were characterized and designated CYP2N22-23, CYP2AD12, and CYP2P16-20. Gene synteny analysis confirmed that the cluster in K. marmoratus is similar to that found in other teleost fishes, including zebrafish. A gene duplication event with diverged catalytic function was observed in CYP2AD12. Moreover, a high level of divergence in expression was observed among the co-localized genes. Phylogeny of the cluster suggested an orthologous relationship with similar genes in zebrafish and Japanese medaka. Gene expression analysis showed that CYP2P19 and CYP2N20 were consecutively expressed throughout embryonic development, whereas CYP2P18 was expressed in all adult tissues, suggesting that members of each CYP2 gene family have different physiological roles even though they are located in the same cluster. Among endocrine-disrupting chemicals (EDCs), benzo[α]pyrene (B[α]P) induced expression of CYP2N23, bisphenol A (BPA) induced CYP2P18 and CYP2P19, and 4-octylphenol (OP) induced CYP2AD12, but there was no significant response to 4-nonylphenol (NP), implying differential catalytic roles of the enzyme. In this paper, we identify and characterize a CYP2 gene cluster in the mangrove killifish K. marmoratus with differing catalytic roles toward EDCs. Our findings provide insights on the roles of nine co-localized CYP2 genes and their catalytic functions for better understanding of chemical-biological interactions in fish. Copyright © 2017 Elsevier B.V. All rights reserved.

Intra- and interspecies gene expression models for predicting drug response in canine osteosarcoma.

Science.gov (United States)

Fowles, Jared S; Brown, Kristen C; Hess, Ann M; Duval, Dawn L; Gustafson, Daniel L

2016-02-19

Genomics-based predictors of drug response have the potential to improve outcomes associated with cancer therapy. Osteosarcoma (OS), the most common primary bone cancer in dogs, is commonly treated with adjuvant doxorubicin or carboplatin following amputation of the affected limb. We evaluated the use of gene-expression based models built in an intra- or interspecies manner to predict chemosensitivity and treatment outcome in canine OS. Models were built and evaluated using microarray gene expression and drug sensitivity data from human and canine cancer cell lines, and canine OS tumor datasets. The "COXEN" method was utilized to filter gene signatures between human and dog datasets based on strong co-expression patterns. Models were built using linear discriminant analysis via the misclassification penalized posterior algorithm. The best doxorubicin model involved genes identified in human lines that were co-expressed and trained on canine OS tumor data, which accurately predicted clinical outcome in 73 % of dogs (p = 0.0262, binomial). The best carboplatin model utilized canine lines for gene identification and model training, with canine OS tumor data for co-expression. Dogs whose treatment matched our predictions had significantly better clinical outcomes than those that didn't (p = 0.0006, Log Rank), and this predictor significantly associated with longer disease free intervals in a Cox multivariate analysis (hazard ratio = 0.3102, p = 0.0124). Our data show that intra- and interspecies gene expression models can successfully predict response in canine OS, which may improve outcome in dogs and serve as pre-clinical validation for similar methods in human cancer research.

Eurotrac: a co-ordinated project for applied tropospheric research

Energy Technology Data Exchange (ETDEWEB)

Borrell, P. [EUROTRAC International Scientific Secretariat, Garmisch-Partenkirchen (Germany)

1995-12-31

It was with the realisation that the scientific problems associated with regional air pollution could only be solved within the framework of an international interdisciplinary approach that in 1985 EUROTRAC, the European co-ordinated research project, was formed. Such an approach provides the scientific consensus necessary for the acceptance of regional air-pollution abatement measures by the countries affected. EUROTRAC is a EUREKA environmental project, studying the transport and chemical transformation of trace substances and pollutants in the troposphere. Three goals were specified the outset: (1) to increase the basic knowledge in atmospheric science, (2) to promote the technological development of sensitive, specific and fast response instruments for environmental research and development, and (3) to improve the scientific basis for taking future political decisions on environmental management in the European countries. Thus EUROTRAC was founded as a scientific project but had the specific intention that its results should be utilised in the formulation of policy. This presentation reviews the progress made towards each of the three goals and also indicates the proposed direction which a follow-on project is likely to take when EUROTRAC finishes at the end of 1995. (author)

Eurotrac: a co-ordinated project for applied tropospheric research

Energy Technology Data Exchange (ETDEWEB)

Borrell, P [EUROTRAC International Scientific Secretariat, Garmisch-Partenkirchen (Germany)

1996-12-31

It was with the realisation that the scientific problems associated with regional air pollution could only be solved within the framework of an international interdisciplinary approach that in 1985 EUROTRAC, the European co-ordinated research project, was formed. Such an approach provides the scientific consensus necessary for the acceptance of regional air-pollution abatement measures by the countries affected. EUROTRAC is a EUREKA environmental project, studying the transport and chemical transformation of trace substances and pollutants in the troposphere. Three goals were specified the outset: (1) to increase the basic knowledge in atmospheric science, (2) to promote the technological development of sensitive, specific and fast response instruments for environmental research and development, and (3) to improve the scientific basis for taking future political decisions on environmental management in the European countries. Thus EUROTRAC was founded as a scientific project but had the specific intention that its results should be utilised in the formulation of policy. This presentation reviews the progress made towards each of the three goals and also indicates the proposed direction which a follow-on project is likely to take when EUROTRAC finishes at the end of 1995. (author)

Improving yield and nitrogen fixation of grain legumes in the tropics and sub-tropics of Asia. Results of a co-ordinated research programme

International Nuclear Information System (INIS)

1998-07-01

The Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture initiated a Co-ordinated Research Project on The Use of Isotopes in Studies to Improve Yield and N 2 Fixation of Grain Legumes with the Aim of Increasing Food Production and Saving N-fertilizer in the Tropics and Sub-Tropics of Asia that was operational from 1990 to 1995. This Project was underpinned by extensive experience in the use of 15 N-labelled fertilizer in quantifying N 2 fixation by food and pasture legumes; the isotope-dilution technique, recognized as the most accurate mode of quantifying fixation, was developed at the IAEA and has been used profitably for over 20 years in co-ordinated research projects that were focused on aspects relevant to the sustainability of agriculture in developing countries in which food security is most under threat. This effort to improve N 2 fixation by food legumes in Asia, and in so doing to increase productivity of cereal-based farming systems as a whole, was timely in terms of regional needs. It was complemented by an overlapping Co-ordinated Research Project entitled ''The Use of Nuclear and Related Techniques in Management of Nitrogen Fixation by trees for Enhancing Soil Fertility and Soil Conservation in Fragile Tropical Soils''. The project involved scientists from Australia, Bangladesh, China, India, Malaysia, Pakistan the Philippines, Sri Lanka, Thailand and Viet Nam

A co-ordinate system for reactor physics calculations in hexagonal geometry

International Nuclear Information System (INIS)

Burte, D.P.

1990-01-01

A method for generating all the geometric information concerning typical reactor physics calculations for a basically hexagonal reactor core or its sector involving any of the possible symmetries is presented. The geometrically allowed symmetries for regular hexagons are discussed. The approach is based on the choice of a suitable co-ordinate system, viz. one using three coplanar (including one redundant) axes, each at 120 0 with its cyclically preceding one. A code named KEKULE' is developed for a 2-D, finite difference, one-group diffusion analysis of a hexagonal core using the approach. It can cater to a full hexagonal core as well as to any symmetric sectorial part of it. The main feature of the code is that the input concerning geometry is a bare minimum. It is hoped that the approach presented will be useful even for the calculations for hexagonal fuel assemblies. (author)

Imaging gene expression in gene therapy

International Nuclear Information System (INIS)

Wiebe, Leonard I.

1997-01-01

Full text. Gene therapy can be used to introduce new genes, or to supplement the function of indigenous genes. At the present time, however, there is non-invasive test to demonstrate efficacy of the gene transfer and expression processes. It has been postulated that scintigraphic imaging can offer unique information on both the site at which the transferred gene is expressed, and the degree of expression, both of which are critical issue for safety and clinical efficacy. Many current studies are based on 'suicide gene therapy' of cancer. Cells modified to express these genes commit metabolic suicide in the presence of an enzyme encoded by the transferred gene and a specifically-convertible pro drug. Pro drug metabolism can lead to selective metabolic trapping, required for scintigraphy. Herpes simplex virus type-1 thymidine kinase (H S V-1 t k + ) has been use for 'suicide' in vivo tumor gene therapy. It has been proposed that radiolabelled nucleosides can be used as radiopharmaceuticals to detect H S V-1 t k + gene expression where the H S V-1 t k + gene serves a reporter or therapeutic function. Animal gene therapy models have been studied using purine-([ 18 F]F H P G; [ 18 F]-A C V), and pyrimidine- ([ 123 / 131 I]I V R F U; [ 124 / 131I ]) antiviral nucleosides. Principles of gene therapy and gene therapy imaging will be reviewed and experimental data for [ 123 / 131I ]I V R F U imaging with the H S V-1 t k + reporter gene will be presented

In vitro mutation breeding of bananas and plantains. Final reports of an FAO/IAEA co-ordinated research programme from 1988 to 1993

International Nuclear Information System (INIS)

1995-06-01

This document contains 9 final reports of the participants at the FAO/IAEA co-ordinated research programme on 'In vitro mutation breeding of bananas and plantains'. A separate abstract was prepared for each report. Refs, figs and tabs

In vitro mutation breeding of bananas and plantains. Final reports of an FAO/IAEA co-ordinated research programme from 1988 to 1993

Energy Technology Data Exchange (ETDEWEB)

NONE

1995-06-01

This document contains 9 final reports of the participants at the FAO/IAEA co-ordinated research programme on `In vitro mutation breeding of bananas and plantains`. A separate abstract was prepared for each report. Refs, figs and tabs.

Co-expression analysis identifies CRC and AP1 the regulator of Arabidopsis fatty acid biosynthesis.

Science.gov (United States)

Han, Xinxin; Yin, Linlin; Xue, Hongwei

2012-07-01

Fatty acids (FAs) play crucial rules in signal transduction and plant development, however, the regulation of FA metabolism is still poorly understood. To study the relevant regulatory network, fifty-eight FA biosynthesis genes including de novo synthases, desaturases and elongases were selected as "guide genes" to construct the co-expression network. Calculation of the correlation between all Arabidopsis thaliana (L.) genes with each guide gene by Arabidopsis co-expression dating mining tools (ACT) identifies 797 candidate FA-correlated genes. Gene ontology (GO) analysis of these co-expressed genes showed they are tightly correlated to photosynthesis and carbohydrate metabolism, and function in many processes. Interestingly, 63 transcription factors (TFs) were identified as candidate FA biosynthesis regulators and 8 TF families are enriched. Two TF genes, CRC and AP1, both correlating with 8 FA guide genes, were further characterized. Analyses of the ap1 and crc mutant showed the altered total FA composition of mature seeds. The contents of palmitoleic acid, stearic acid, arachidic acid and eicosadienoic acid are decreased, whereas that of oleic acid is increased in ap1 and crc seeds, which is consistent with the qRT-PCR analysis revealing the suppressed expression of the corresponding guide genes. In addition, yeast one-hybrid analysis and electrophoretic mobility shift assay (EMSA) revealed that CRC can bind to the promoter regions of KCS7 and KCS15, indicating that CRC may directly regulate FA biosynthesis. © 2012 Institute of Botany, Chinese Academy of Sciences.

Tumor-produced, active Interleukin-1 β regulates gene expression in carcinoma-associated fibroblasts

International Nuclear Information System (INIS)

Dudas, Jozsef; Fullar, Alexandra; Bitsche, Mario; Schartinger, Volker; Kovalszky, Ilona; Sprinzl, Georg Mathias; Riechelmann, Herbert

2011-01-01

Recently we described a co-culture model of periodontal ligament (PDL) fibroblasts and SCC-25 lingual squamous carcinoma cells, which resulted in conversion of normal fibroblasts into carcinoma-associated fibroblasts (CAFs), and in epithelial-mesenchymal transition (EMT) of SCC-25 cells. We have found a constitutive high interleukin-1β (IL1-β) expression in SCC-25 cells in normal and in co-cultured conditions. In our hypothesis a constitutive IL1-β expression in SCC-25 regulates gene expression in fibroblasts during co-culture. Co-cultures were performed between PDL fibroblasts and SCC-25 cells with and without dexamethasone (DEX) treatment; IL1-β processing was investigated in SCC-25 cells, tumor cells and PDL fibroblasts were treated with IL1-β. IL1-β signaling was investigated by western blot and immunocytochemistry. IL1-β-regulated genes were analyzed by real-time qPCR. SCC-25 cells produced 16 kD active IL1-β, its receptor was upregulated in PDL fibroblasts during co-culture, which induced phosphorylation of interleukin-1 receptor-associated kinase-1 (IRAK-1), and nuclear translocalization of NFκBα. Several genes, including interferon regulatory factor 1 (IRF1) interleukin-6 (IL-6) and prostaglandin-endoperoxide synthase 2 (COX-2) were induced in CAFs during co-culture. The most enhanced induction was found for IL-6 and COX-2. Treatment of PDL fibroblasts with IL1-β reproduced a time- and dose-dependent upregulation of IL1-receptor, IL-6 and COX-2. A further proof was achieved by DEX inhibition for IL1-β-stimulated IL-6 and COX-2 gene expression. Constitutive expression of IL1-β in the tumor cells leads to IL1-β-stimulated gene expression changes in tumor-associated fibroblasts, which are involved in tumor progression. -- Graphical abstract: SCC-25 cells produce active, processed IL1-β. PDL fibroblasts possess receptor for IL1-β, and its expression is increased 4.56-times in the presence of SCC-25 tumor cells. IL1-β receptor expression in

Tumor-produced, active Interleukin-1 {beta} regulates gene expression in carcinoma-associated fibroblasts

Energy Technology Data Exchange (ETDEWEB)

Dudas, Jozsef, E-mail: Jozsef.Dudas@i-med.ac.at [Department of Otorhinolaryngology, Medical University Innsbruck, Anichstrasse 35, A-6020 Innsbruck (Austria); Fullar, Alexandra, E-mail: fullarsz@gmail.com [Department of Otorhinolaryngology, Medical University Innsbruck, Anichstrasse 35, A-6020 Innsbruck (Austria); 1st Institute of Pathology and Experimental Cancer Research, Semmelweis University, Ulloei ut 26, H-1085 Budapest (Hungary); Bitsche, Mario, E-mail: Mario.Bitsche@i-med.ac.at [Department of Otorhinolaryngology, Medical University Innsbruck, Anichstrasse 35, A-6020 Innsbruck (Austria); Schartinger, Volker, E-mail: Volker.Schartinger@i-med.ac.at [Department of Otorhinolaryngology, Medical University Innsbruck, Anichstrasse 35, A-6020 Innsbruck (Austria); Kovalszky, Ilona, E-mail: koval@korb1.sote.hu [1st Institute of Pathology and Experimental Cancer Research, Semmelweis University, Ulloei ut 26, H-1085 Budapest (Hungary); Sprinzl, Georg Mathias, E-mail: Georg.Sprinzl@i-med.ac.at [Department of Otorhinolaryngology, Medical University Innsbruck, Anichstrasse 35, A-6020 Innsbruck (Austria); Riechelmann, Herbert, E-mail: Herbert.Riechelmann@i-med.ac.at [Department of Otorhinolaryngology, Medical University Innsbruck, Anichstrasse 35, A-6020 Innsbruck (Austria)

2011-09-10

Recently we described a co-culture model of periodontal ligament (PDL) fibroblasts and SCC-25 lingual squamous carcinoma cells, which resulted in conversion of normal fibroblasts into carcinoma-associated fibroblasts (CAFs), and in epithelial-mesenchymal transition (EMT) of SCC-25 cells. We have found a constitutive high interleukin-1{beta} (IL1-{beta}) expression in SCC-25 cells in normal and in co-cultured conditions. In our hypothesis a constitutive IL1-{beta} expression in SCC-25 regulates gene expression in fibroblasts during co-culture. Co-cultures were performed between PDL fibroblasts and SCC-25 cells with and without dexamethasone (DEX) treatment; IL1-{beta} processing was investigated in SCC-25 cells, tumor cells and PDL fibroblasts were treated with IL1-{beta}. IL1-{beta} signaling was investigated by western blot and immunocytochemistry. IL1-{beta}-regulated genes were analyzed by real-time qPCR. SCC-25 cells produced 16 kD active IL1-{beta}, its receptor was upregulated in PDL fibroblasts during co-culture, which induced phosphorylation of interleukin-1 receptor-associated kinase-1 (IRAK-1), and nuclear translocalization of NF{kappa}B{alpha}. Several genes, including interferon regulatory factor 1 (IRF1) interleukin-6 (IL-6) and prostaglandin-endoperoxide synthase 2 (COX-2) were induced in CAFs during co-culture. The most enhanced induction was found for IL-6 and COX-2. Treatment of PDL fibroblasts with IL1-{beta} reproduced a time- and dose-dependent upregulation of IL1-receptor, IL-6 and COX-2. A further proof was achieved by DEX inhibition for IL1-{beta}-stimulated IL-6 and COX-2 gene expression. Constitutive expression of IL1-{beta} in the tumor cells leads to IL1-{beta}-stimulated gene expression changes in tumor-associated fibroblasts, which are involved in tumor progression. -- Graphical abstract: SCC-25 cells produce active, processed IL1-{beta}. PDL fibroblasts possess receptor for IL1-{beta}, and its expression is increased 4.56-times in the

Identification of differentially expressed genes in flax (Linum usitatissimum L.) under saline-alkaline stress by digital gene expression.

Science.gov (United States)

Yu, Ying; Huang, Wengong; Chen, Hongyu; Wu, Guangwen; Yuan, Hongmei; Song, Xixia; Kang, Qinghua; Zhao, Dongsheng; Jiang, Weidong; Liu, Yan; Wu, Jianzhong; Cheng, Lili; Yao, Yubo; Guan, Fengzhi

2014-10-01

The salinization and alkalization of soil are widespread environmental problems, and alkaline salt stress is more destructive than neutral salt stress. Therefore, understanding the mechanism of plant tolerance to saline-alkaline stress has become a major challenge. However, little attention has been paid to the mechanism of plant alkaline salt tolerance. In this study, gene expression profiling of flax was analyzed under alkaline-salt stress (AS2), neutral salt stress (NSS) and alkaline stress (AS) by digital gene expression. Three-week-old flax seedlings were placed in 25 mM Na2CO3 (pH11.6) (AS2), 50mM NaCl (NSS) and NaOH (pH11.6) (AS) for 18 h. There were 7736, 1566 and 454 differentially expressed genes in AS2, NSS and AS compared to CK, respectively. The GO category gene enrichment analysis revealed that photosynthesis was particularly affected in AS2, carbohydrate metabolism was particularly affected in NSS, and the response to biotic stimulus was particularly affected in AS. We also analyzed the expression pattern of five categories of genes including transcription factors, signaling transduction proteins, phytohormones, reactive oxygen species proteins and transporters under these three stresses. Some key regulatory gene families involved in abiotic stress, such as WRKY, MAPKKK, ABA, PrxR and ion channels, were differentially expressed. Compared with NSS and AS, AS2 triggered more differentially expressed genes and special pathways, indicating that the mechanism of AS2 was more complex than NSS and AS. To the best of our knowledge, this was the first transcriptome analysis of flax in response to saline-alkaline stress. These data indicate that common and diverse features of saline-alkaline stress provide novel insights into the molecular mechanisms of plant saline-alkaline tolerance and offer a number of candidate genes as potential markers of tolerance to saline-alkaline stress. Copyright © 2014 Elsevier B.V. All rights reserved.

Summary report of the third research co-ordination meeting on measurement, calculation and evaluation of photon production data

International Nuclear Information System (INIS)

Oblozinsky, P.

1998-01-01

The present report contains the account of the last meeting of the Co-ordinated Research Project on ''Measurement, Calculation and Evaluation of Photon Production Data''. In addition to the summary of the meeting, the overall results achieved under the project in 1994-1997 are summarized, including the list of publications. The status of work on the Final Report of the project is also given. (author)

Extensive co-operation between the Epstein-Barr virus EBNA3 proteins in the manipulation of host gene expression and epigenetic chromatin modification.

Directory of Open Access Journals (Sweden)

Robert E White

2010-11-01

Full Text Available Epstein-Barr virus (EBV is able to drive the transformation of B-cells, resulting in the generation of lymphoblastoid cell lines (LCLs in vitro. EBV nuclear proteins EBNA3A and EBNA3C are necessary for efficient transformation, while EBNA3B is dispensable. We describe a transcriptome analysis of BL31 cells infected with a series of EBNA3-knockout EBVs, including one deleted for all three EBNA3 genes. Using Affymetrix Exon 1.0 ST microarrays analysed with the MMBGX algorithm, we have identified over 1000 genes whose regulation by EBV requires one of the EBNA3s. Remarkably, a third of the genes identified require more than one EBNA3 for their regulation, predominantly EBNA3C co-operating with either EBNA3B, EBNA3A or both. The microarray was validated by real-time PCR, while ChIP analysis of a selection of co-operatively repressed promoters indicates a role for polycomb group complexes. Targets include genes involved in apoptosis, cell migration and B-cell differentiation, and show a highly significant but subtle alteration in genes involved in mitosis. In order to assess the relevance of the BL31 system to LCLs, we analysed the transcriptome of a set of EBNA3B knockout (3BKO LCLs. Around a third of the genes whose expression level in LCLs was altered in the absence of EBNA3B were also altered in 3BKO-BL31 cell lines.Among these are TERT and TCL1A, implying that EBV-induced changes in the expression of these genes are not required for B-cell transformation. We also identify 26 genes that require both EBNA3A and EBNA3B for their regulation in LCLs. Together, this shows the complexity of the interaction between EBV and its host, whereby multiple EBNA3 proteins co-operate to modulate the behaviour of the host cell.

Meta-analysis of inter-species liver co-expression networks elucidates traits associated with common human diseases.

Directory of Open Access Journals (Sweden)

Kai Wang

2009-12-01

Full Text Available Co-expression networks are routinely used to study human diseases like obesity and diabetes. Systematic comparison of these networks between species has the potential to elucidate common mechanisms that are conserved between human and rodent species, as well as those that are species-specific characterizing evolutionary plasticity. We developed a semi-parametric meta-analysis approach for combining gene-gene co-expression relationships across expression profile datasets from multiple species. The simulation results showed that the semi-parametric method is robust against noise. When applied to human, mouse, and rat liver co-expression networks, our method out-performed existing methods in identifying gene pairs with coherent biological functions. We identified a network conserved across species that highlighted cell-cell signaling, cell-adhesion and sterol biosynthesis as main biological processes represented in genome-wide association study candidate gene sets for blood lipid levels. We further developed a heterogeneity statistic to test for network differences among multiple datasets, and demonstrated that genes with species-specific interactions tend to be under positive selection throughout evolution. Finally, we identified a human-specific sub-network regulated by RXRG, which has been validated to play a different role in hyperlipidemia and Type 2 diabetes between human and mouse. Taken together, our approach represents a novel step forward in integrating gene co-expression networks from multiple large scale datasets to leverage not only common information but also differences that are dataset-specific.

Rhythmic diel pattern of gene expression in juvenile maize leaf.

Directory of Open Access Journals (Sweden)

Maciej Jończyk

Full Text Available BACKGROUND: Numerous biochemical and physiological parameters of living organisms follow a circadian rhythm. Although such rhythmic behavior is particularly pronounced in plants, which are strictly dependent on the daily photoperiod, data on the molecular aspects of the diurnal cycle in plants is scarce and mostly concerns the model species Arabidopsis thaliana. Here we studied the leaf transcriptome in seedlings of maize, an important C4 crop only distantly related to A. thaliana, throughout a cycle of 10 h darkness and 14 h light to look for rhythmic patterns of gene expression. RESULTS: Using DNA microarrays comprising ca. 43,000 maize-specific probes we found that ca. 12% of all genes showed clear-cut diel rhythms of expression. Cluster analysis identified 35 groups containing from four to ca. 1,000 genes, each comprising genes of similar expression patterns. Perhaps unexpectedly, the most pronounced and most common (concerning the highest number of genes expression maxima were observed towards and during the dark phase. Using Gene Ontology classification several meaningful functional associations were found among genes showing similar diel expression patterns, including massive induction of expression of genes related to gene expression, translation, protein modification and folding at dusk and night. Additionally, we found a clear-cut tendency among genes belonging to individual clusters to share defined transcription factor-binding sequences. CONCLUSIONS: Co-expressed genes belonging to individual clusters are likely to be regulated by common mechanisms. The nocturnal phase of the diurnal cycle involves gross induction of fundamental biochemical processes and should be studied more thoroughly than was appreciated in most earlier physiological studies. Although some general mechanisms responsible for the diel regulation of gene expression might be shared among plants, details of the diurnal regulation of gene expression seem to differ

Gene co-expression networks in liver and muscle transcriptome reveal sex-specific gene expression in lambs fed with a mix of essential oils

DEFF Research Database (Denmark)

Sabino, Marcella; Carmelo, Victor Adriano Okstoft; Mazzoni, Gianluca

2018-01-01

the potential of RNA-Sequencing data in order to evaluate the effect of an EO supplementary diet on gene expression in both lamb liver and muscle. Using a treatment and sex interaction model, 13 and 4 differentially expressed genes were identified in liver and muscle respectively. Sex-specific differentially...... on the expression profile of both liver and muscle tissues. We hypothesize that the presence of EOs could have beneficial effects on wellness of male lamb and further analyses are needed to understand the biological mechanisms behind the different effect of EO metabolites based on sex. Using lamb as a model...

Determining Physical Mechanisms of Gene Expression Regulation from Single Cell Gene Expression Data

OpenAIRE

Ezer, Daphne; Moignard, Victoria; G?ttgens, Berthold; Adryan, Boris

2016-01-01

Many genes are expressed in bursts, which can contribute to cell-to-cell heterogeneity. It is now possible to measure this heterogeneity with high throughput single cell gene expression assays (single cell qPCR and RNA-seq). These experimental approaches generate gene expression distributions which can be used to estimate the kinetic parameters of gene expression bursting, namely the rate that genes turn on, the rate that genes turn off, and the rate of transcription. We construct a complete ...

Imaging gene expression in gene therapy

Energy Technology Data Exchange (ETDEWEB)

Wiebe, Leonard I. [Alberta Univ., Edmonton (Canada). Noujaim Institute for Pharmaceutical Oncology Research

1997-12-31

Full text. Gene therapy can be used to introduce new genes, or to supplement the function of indigenous genes. At the present time, however, there is non-invasive test to demonstrate efficacy of the gene transfer and expression processes. It has been postulated that scintigraphic imaging can offer unique information on both the site at which the transferred gene is expressed, and the degree of expression, both of which are critical issue for safety and clinical efficacy. Many current studies are based on `suicide gene therapy` of cancer. Cells modified to express these genes commit metabolic suicide in the presence of an enzyme encoded by the transferred gene and a specifically-convertible pro drug. Pro drug metabolism can lead to selective metabolic trapping, required for scintigraphy. Herpes simplex virus type-1 thymidine kinase (H S V-1 t k{sup +}) has been use for `suicide` in vivo tumor gene therapy. It has been proposed that radiolabelled nucleosides can be used as radiopharmaceuticals to detect H S V-1 t k{sup +} gene expression where the H S V-1 t k{sup +} gene serves a reporter or therapeutic function. Animal gene therapy models have been studied using purine-([{sup 18} F]F H P G; [{sup 18} F]-A C V), and pyrimidine- ([{sup 123}/{sup 131} I]I V R F U; [{sup 124}/{sup 131I}]) antiviral nucleosides. Principles of gene therapy and gene therapy imaging will be reviewed and experimental data for [{sup 123}/{sup 131I}]I V R F U imaging with the H S V-1 t k{sup +} reporter gene will be presented

Case of cholera preparedness, response and prevention in the SADC region: A need for proactive and multi-level communication and co-ordination

CSIR Research Space (South Africa)

Said, MD

2011-10-01

Full Text Available In this paper the authors seek to identify the most appropriate model for a regional co-ordination mechanism for cholera preparedness, response and prevention. The qualitative mixed-method data collection approach that was followed revealed the need...

The fourth UNDP/RCA/IAEA/meeting of national co-ordinators for radiation technology. Report

International Nuclear Information System (INIS)

1996-01-01

The objectives of the Meeting were to provide information for the Terminal Report of the joint UNDP/RCA/IAEA project RAS/92/073 and to look into future activities under the Radiation Technology project. The main achievements of this Meeting are: The Meeting reviewed the implementation of all radiation technology sub-projects and agreed that all of them were successful but not yet equally developed among RCA Member States. The Meeting recommended to have three projects carried out in the form of Co-ordinated Research Programs and requested the IAEA to find new ways to implement the organized in RCA Member States to carry these CRPs out. Figs, tabs

Nuclear techniques in the coal industry. Proceedings of a final research co-ordination meeting

Energy Technology Data Exchange (ETDEWEB)

NONE

1995-11-01

With the aim of promoting advanced research and facilitating a more extensive application of nuclear techniques for environmental protection in the exploration and exploitation of coal, the IAEA established the present co-ordinated research programme (CRP) in 1989. This report includes an assessment of the current status and trends in nuclear techniques in the coal industry and the results obtained by the participants at the CRP. Proceedings of the final CRP on ``Nuclear Techniques in Exploration and Exploitation of Coal: On-line and Bulk Analysis and Evaluation of Potential Environmental Pollutants in Coal and Coke``, was held in Krakow, Poland, from 9 to 12 May 1994. Refs, figs, tabs.

A systematic review of instruments for assessment of capacity in activities of daily living in children with developmental co-ordination disorder

NARCIS (Netherlands)

van der Linde, B W; van Netten, J J; Otten, E; Postema, K; Geuze, R H; Schoemaker, M M

Children with developmental co-ordination disorder (DCD) face evident motor difficulties in activities of daily living (ADL). Assessment of their capacity in ADL is essential for diagnosis and intervention, in order to limit the daily consequences of the disorder. The aim of this study is to

dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface

Science.gov (United States)

Rot, Gregor; Parikh, Anup; Curk, Tomaz; Kuspa, Adam; Shaulsky, Gad; Zupan, Blaz

2009-01-01

Background Bioinformatics often leverages on recent advancements in computer science to support biologists in their scientific discovery process. Such efforts include the development of easy-to-use web interfaces to biomedical databases. Recent advancements in interactive web technologies require us to rethink the standard submit-and-wait paradigm, and craft bioinformatics web applications that share analytical and interactive power with their desktop relatives, while retaining simplicity and availability. Results We have developed dictyExpress, a web application that features a graphical, highly interactive explorative interface to our database that consists of more than 1000 Dictyostelium discoideum gene expression experiments. In dictyExpress, the user can select experiments and genes, perform gene clustering, view gene expression profiles across time, view gene co-expression networks, perform analyses of Gene Ontology term enrichment, and simultaneously display expression profiles for a selected gene in various experiments. Most importantly, these tasks are achieved through web applications whose components are seamlessly interlinked and immediately respond to events triggered by the user, thus providing a powerful explorative data analysis environment. Conclusion dictyExpress is a precursor for a new generation of web-based bioinformatics applications with simple but powerful interactive interfaces that resemble that of the modern desktop. While dictyExpress serves mainly the Dictyostelium research community, it is relatively easy to adapt it to other datasets. We propose that the design ideas behind dictyExpress will influence the development of similar applications for other model organisms. PMID:19706156

A Genome-Wide Association Study for Culm Cellulose Content in Barley Reveals Candidate Genes Co-Expressed with Members of the CELLULOSE SYNTHASE A Gene Family

Science.gov (United States)

Houston, Kelly; Burton, Rachel A.; Sznajder, Beata; Rafalski, Antoni J.; Dhugga, Kanwarpal S.; Mather, Diane E.; Taylor, Jillian; Steffenson, Brian J.; Waugh, Robbie; Fincher, Geoffrey B.

2015-01-01

Cellulose is a fundamentally important component of cell walls of higher plants. It provides a scaffold that allows the development and growth of the plant to occur in an ordered fashion. Cellulose also provides mechanical strength, which is crucial for both normal development and to enable the plant to withstand both abiotic and biotic stresses. We quantified the cellulose concentration in the culm of 288 two – rowed and 288 six – rowed spring type barley accessions that were part of the USDA funded barley Coordinated Agricultural Project (CAP) program in the USA. When the population structure of these accessions was analysed we identified six distinct populations, four of which we considered to be comprised of a sufficient number of accessions to be suitable for genome-wide association studies (GWAS). These lines had been genotyped with 3072 SNPs so we combined the trait and genetic data to carry out GWAS. The analysis allowed us to identify regions of the genome containing significant associations between molecular markers and cellulose concentration data, including one region cross-validated in multiple populations. To identify candidate genes we assembled the gene content of these regions and used these to query a comprehensive RNA-seq based gene expression atlas. This provided us with gene annotations and associated expression data across multiple tissues, which allowed us to formulate a supported list of candidate genes that regulate cellulose biosynthesis. Several regions identified by our analysis contain genes that are co-expressed with CELLULOSE SYNTHASE A (HvCesA) across a range of tissues and developmental stages. These genes are involved in both primary and secondary cell wall development. In addition, genes that have been previously linked with cellulose synthesis by biochemical methods, such as HvCOBRA, a gene of unknown function, were also associated with cellulose levels in the association panel. Our analyses provide new insights into the

A Special Extract of Bacopa monnieri (CDRI-08-Restored Memory in CoCl2-Hypoxia Mimetic Mice Is Associated with Upregulation of Fmr-1 Gene Expression in Hippocampus

Directory of Open Access Journals (Sweden)

Anupama Rani

2015-01-01

Full Text Available Fragile X mental retardation protein (FMRP is a neuronal translational repressor and has been implicated in learning, memory, and cognition. However, the role of Bacopa monnieri extract (CDRI-08 in enhancing cognitive abilities in hypoxia-induced memory impairment via Fmr-1 gene expression is not known. Here, we have studied effects of CDRI-08 on the expression of Fmr-1 gene in the hippocampus of well validated cobalt chloride (CoCl2-induced hypoxia mimetic mice and analyzed the data with alterations in spatial memory. Results obtained from Morris water maze test suggest that CoCl2 treatment causes severe loss of spatial memory and CDRI-08 is capable of reversing it towards that in the normal control mice. Our semiquantitative RT-PCR, Western blot, and immunofluorescence microscopic data reveal that CoCl2-induced hypoxia significantly upregulates the expression of Hif-1α and downregulates the Fmr-1 expression in the hippocampus, respectively. Further, CDRI-08 administration reverses the memory loss and this is correlated with significant downregulation of Hif-1α and upregulation of Fmr-1 expression. Our data are novel and may provide mechanisms of hypoxia-induced impairments in the spatial memory and action of CDRI-08 in the recovery of hypoxia led memory impairment involving Fmr-1 gene encoded protein called FMRP.

Down-Regulation of Gene Expression by RNA-Induced Gene Silencing

Science.gov (United States)

Travella, Silvia; Keller, Beat

Down-regulation of endogenous genes via post-transcriptional gene silencing (PTGS) is a key to the characterization of gene function in plants. Many RNA-based silencing mechanisms such as post-transcriptional gene silencing, co-suppression, quelling, and RNA interference (RNAi) have been discovered among species of different kingdoms (plants, fungi, and animals). One of the most interesting discoveries was RNAi, a sequence-specific gene-silencing mechanism initiated by the introduction of double-stranded RNA (dsRNA), homologous in sequence to the silenced gene, which triggers degradation of mRNA. Infection of plants with modified viruses can also induce RNA silencing and is referred to as virus-induced gene silencing (VIGS). In contrast to insertional mutagenesis, these emerging new reverse genetic approaches represent a powerful tool for exploring gene function and for manipulating gene expression experimentally in cereal species such as barley and wheat. We examined how RNAi and VIGS have been used to assess gene function in barley and wheat, including molecular mechanisms involved in the process and available methodological elements, such as vectors, inoculation procedures, and analysis of silenced phenotypes.

The gsdf gene locus harbors evolutionary conserved and clustered genes preferentially expressed in fish previtellogenic oocytes.

Science.gov (United States)

Gautier, Aude; Le Gac, Florence; Lareyre, Jean-Jacques

2011-02-01

display a different cellular localization compared to that of the gsdf gene indicating that the later gene is not co-regulated. Interestingly, our study identifies new clustered genes that are specifically expressed in previtellogenic oocytes (nup54, aff1, klhl8, sdad1). Copyright © 2010 Elsevier B.V. All rights reserved.

Gene Expression Analysis in Tubule Interstitial Compartments Reveals Candidate Agents for IgA Nephropathy

Directory of Open Access Journals (Sweden)

Jinling Wang

2014-09-01

Full Text Available Background/Aims: Our aim was to explore the molecular mechanism underlying development of IgA nephropathy and discover candidate agents for IgA nephropathy. Methods: The differentially expressed genes (DEGs between patients with IgA nephropathy and normal controls were identified by the data of GSE35488 downloaded from GEO (Gene Expression Omnibus database. The co-expressed gene pairs among DEGs were screened to construct the gene-gene interaction network. Gene Ontology (GO enrichment analysis was performed to analyze the functions of DEGs. The biologically active small molecules capable of targeting IgA nephropathy were identified using the Connectivity Map (cMap database. Results: A total of 55 genes involved in response to organic substance, transcription factor activity and response to steroid hormone stimulus were identified to be differentially expressed in IgA nephropathy patients compared to healthy individuals. A network with 45 co-expressed gene pairs was constructed. DEGs in the network were significantly enriched in response to organic substance. Additionally, a group of small molecules were identified, such as doxorubicin and thapsigargin. Conclusion: Our work provided a systematic insight in understanding the mechanism of IgA nephropathy. Small molecules such as thapsigargin might be potential candidate agents for the treatment of IgA nephropathy.

The diurnal logic of the expression of the chloroplast genome in Chlamydomonas reinhardtii.

Directory of Open Access Journals (Sweden)

Adam D Idoine

Full Text Available Chloroplasts are derived from cyanobacteria and have retained a bacterial-type genome and gene expression machinery. The chloroplast genome encodes many of the core components of the photosynthetic apparatus in the thylakoid membranes. To avoid photooxidative damage and production of harmful reactive oxygen species (ROS by incompletely assembled thylakoid protein complexes, chloroplast gene expression must be tightly regulated and co-ordinated with gene expression in the nucleus. Little is known about the control of chloroplast gene expression at the genome-wide level in response to internal rhythms and external cues. To obtain a comprehensive picture of organelle transcript levels in the unicellular model alga Chlamydomonas reinhardtii in diurnal conditions, a qRT-PCR platform was developed and used to quantify 68 chloroplast, 21 mitochondrial as well as 71 nuclear transcripts in cells grown in highly controlled 12 h light/12 h dark cycles. Interestingly, in anticipation of dusk, chloroplast transcripts from genes involved in transcription reached peak levels first, followed by transcripts from genes involved in translation, and finally photosynthesis gene transcripts. This pattern matches perfectly the theoretical demands of a cell "waking up" from the night. A similar trend was observed in the nuclear transcripts. These results suggest a striking internal logic in the expression of the chloroplast genome and a previously unappreciated complexity in the regulation of chloroplast genes.

The Medicago truncatula gene expression atlas web server

Directory of Open Access Journals (Sweden)

Tang Yuhong

2009-12-01

Full Text Available Abstract Background Legumes (Leguminosae or Fabaceae play a major role in agriculture. Transcriptomics studies in the model legume species, Medicago truncatula, are instrumental in helping to formulate hypotheses about the role of legume genes. With the rapid growth of publically available Affymetrix GeneChip Medicago Genome Array GeneChip data from a great range of tissues, cell types, growth conditions, and stress treatments, the legume research community desires an effective bioinformatics system to aid efforts to interpret the Medicago genome through functional genomics. We developed the Medicago truncatula Gene Expression Atlas (MtGEA web server for this purpose. Description The Medicago truncatula Gene Expression Atlas (MtGEA web server is a centralized platform for analyzing the Medicago transcriptome. Currently, the web server hosts gene expression data from 156 Affymetrix GeneChip® Medicago genome arrays in 64 different experiments, covering a broad range of developmental and environmental conditions. The server enables flexible, multifaceted analyses of transcript data and provides a range of additional information about genes, including different types of annotation and links to the genome sequence, which help users formulate hypotheses about gene function. Transcript data can be accessed using Affymetrix probe identification number, DNA sequence, gene name, functional description in natural language, GO and KEGG annotation terms, and InterPro domain number. Transcripts can also be discovered through co-expression or differential expression analysis. Flexible tools to select a subset of experiments and to visualize and compare expression profiles of multiple genes have been implemented. Data can be downloaded, in part or full, in a tabular form compatible with common analytical and visualization software. The web server will be updated on a regular basis to incorporate new gene expression data and genome annotation, and is accessible

Three ancient hormonal cues co-ordinate shoot branching in a moss.

Science.gov (United States)

Coudert, Yoan; Palubicki, Wojtek; Ljung, Karin; Novak, Ondrej; Leyser, Ottoline; Harrison, C Jill

2015-03-25

Shoot branching is a primary contributor to plant architecture, evolving independently in flowering plant sporophytes and moss gametophytes. Mechanistic understanding of branching is largely limited to flowering plants such as Arabidopsis, which have a recent evolutionary origin. We show that in gametophytic shoots of Physcomitrella, lateral branches arise by re-specification of epidermal cells into branch initials. A simple model co-ordinating the activity of leafy shoot tips can account for branching patterns, and three known and ancient hormonal regulators of sporophytic branching interact to generate the branching pattern- auxin, cytokinin and strigolactone. The mode of auxin transport required in branch patterning is a key divergence point from known sporophytic pathways. Although PIN-mediated basipetal auxin transport regulates branching patterns in flowering plants, this is not so in Physcomitrella, where bi-directional transport is required to generate realistic branching patterns. Experiments with callose synthesis inhibitors suggest plasmodesmal connectivity as a potential mechanism for transport.

Comparison of gene co-networks reveals the molecular mechanisms of the rice (Oryza sativa L.) response to Rhizoctonia solani AG1 IA infection.

Science.gov (United States)

Zhang, Jinfeng; Zhao, Wenjuan; Fu, Rong; Fu, Chenglin; Wang, Lingxia; Liu, Huainian; Li, Shuangcheng; Deng, Qiming; Wang, Shiquan; Zhu, Jun; Liang, Yueyang; Li, Ping; Zheng, Aiping

2018-05-05

Rhizoctonia solani causes rice sheath blight, an important disease affecting the growth of rice (Oryza sativa L.). Attempts to control the disease have met with little success. Based on transcriptional profiling, we previously identified more than 11,947 common differentially expressed genes (TPM > 10) between the rice genotypes TeQing and Lemont. In the current study, we extended these findings by focusing on an analysis of gene co-expression in response to R. solani AG1 IA and identified gene modules within the networks through weighted gene co-expression network analysis (WGCNA). We compared the different genes assigned to each module and the biological interpretations of gene co-expression networks at early and later modules in the two rice genotypes to reveal differential responses to AG1 IA. Our results show that different changes occurred in the two rice genotypes and that the modules in the two groups contain a number of candidate genes possibly involved in pathogenesis, such as the VQ protein. Furthermore, these gene co-expression networks provide comprehensive transcriptional information regarding gene expression in rice in response to AG1 IA. The co-expression networks derived from our data offer ideas for follow-up experimentation that will help advance our understanding of the translational regulation of rice gene expression changes in response to AG1 IA.

Application of DNA based marker mutations for improvement of cereals and other sexually reproduced crop plants. Proceedings of a final research co-ordination meeting

Energy Technology Data Exchange (ETDEWEB)

NONE

1998-03-01

The Co-ordinated Research Programme (CRP) on the Application of DNA Based Marker Mutations for Improvement of Cereals and Other Sexually Reproduced Crop Plants represents the first of three CRPs dealing with the application of molecular markers to mutations and plant breeding and was implemented between 1992 and 1996. A second companion CRP entitled Use of Novel DNA Fingerprinting Techniques for the Detection and Characterization of Genetic Variation in Vegetatively Propagated Crops devoted to the application of molecular markers in vegetatively propagated crops species was implemented between 1993 and 1997. One positive consequence of these two CRPs has been the implementation of a third CRP entitled Radioactively Labeled DNA Probes for Crop Improvement, which began in 1995 and aims to provide enabling technologies, in the form of probes and primers, to laboratories in developing countries. The rapid development of molecular marker technologies has also resulted in a dramatic increase in request from developing Member States for technical co-operation projects utilizing molecular markers to improve local varieties for biotic and abiotic stresses and other traits of relevance. With the intensified use of induced mutations in genetic studies, it will be important to continue the important work of understanding induced mutations at the molecular level. Evidence of the progress made in implementing molecular marker technologies in laboratories around the world is presented in this publication, which contains the results presented by the participants at the fourth and final Research Co-ordination Meeting of the CRP held in Vienna, 4-8 November 1996. The FAO and IAEA wish to express their sincere appreciation to the participants of the meeting for their work during the project period resulting in the summary and scientific reports presented in this publication. Refs, figs, tabs.

Application of DNA based marker mutations for improvement of cereals and other sexually reproduced crop plants. Proceedings of a final research co-ordination meeting

International Nuclear Information System (INIS)

1998-03-01

The Co-ordinated Research Programme (CRP) on the Application of DNA Based Marker Mutations for Improvement of Cereals and Other Sexually Reproduced Crop Plants represents the first of three CRPs dealing with the application of molecular markers to mutations and plant breeding and was implemented between 1992 and 1996. A second companion CRP entitled Use of Novel DNA Fingerprinting Techniques for the Detection and Characterization of Genetic Variation in Vegetatively Propagated Crops devoted to the application of molecular markers in vegetatively propagated crops species was implemented between 1993 and 1997. One positive consequence of these two CRPs has been the implementation of a third CRP entitled Radioactively Labeled DNA Probes for Crop Improvement, which began in 1995 and aims to provide enabling technologies, in the form of probes and primers, to laboratories in developing countries. The rapid development of molecular marker technologies has also resulted in a dramatic increase in request from developing Member States for technical co-operation projects utilizing molecular markers to improve local varieties for biotic and abiotic stresses and other traits of relevance. With the intensified use of induced mutations in genetic studies, it will be important to continue the important work of understanding induced mutations at the molecular level. Evidence of the progress made in implementing molecular marker technologies in laboratories around the world is presented in this publication, which contains the results presented by the participants at the fourth and final Research Co-ordination Meeting of the CRP held in Vienna, 4-8 November 1996. The FAO and IAEA wish to express their sincere appreciation to the participants of the meeting for their work during the project period resulting in the summary and scientific reports presented in this publication

Comparative transcriptome and gene co-expression network analysis reveal genes and signaling pathways adaptively responsive to varied adverse stresses in the insect fungal pathogen, Beauveria bassiana.

Science.gov (United States)

He, Zhangjiang; Zhao, Xin; Lu, Zhuoyue; Wang, Huifang; Liu, Pengfei; Zeng, Fanqin; Zhang, Yongjun

2018-01-01

Sensing, responding, and adapting to the surrounding environment are crucial for all living organisms to survive, proliferate, and differentiate in their biological niches. Beauveria bassiana is an economically important insect-pathogenic fungus which is widely used as a biocontrol agent to control a variety of insect pests. The fungal pathogen unavoidably encounters a variety of adverse environmental stresses and defense response from the host insects during application of the fungal agents. However, few are known about the transcription response of the fungus to respond or adapt varied adverse stresses. Here, we comparatively analyzed the transcriptome of B. bassiana in globe genome under the varied stationary-phase stresses including osmotic agent (0.8 M NaCl), high temperature (32 °C), cell wall-perturbing agent (Congo red), and oxidative agents (H 2 O 2 or menadione). Total of 12,412 reads were obtained, and mapped to the 6767 genes of the B. bassiana. All of these stresses caused transcription responses involved in basal metabolism, cell wall construction, stress response or cell rescue/detoxification, signaling transduction and gene transcription regulation, and likely other cellular processes. An array of genes displayed similar transcription patterns in response to at least two of the five stresses, suggesting a shared transcription response to varied adverse stresses. Gene co-expression network analysis revealed that mTOR signaling pathway, but not HOG1 MAP kinase pathway, played a central role in regulation the varied adverse stress responses, which was verified by RNAi-mediated knockdown of TOR1. Our findings provided an insight of transcription response and gene co-expression network of B. bassiana in adaptation to varied environments. Copyright © 2017 Elsevier Inc. All rights reserved.

Improvements in the quality of co-ordination of nursing care following implementation of the Resident Assessment Instrument in Dutch nursing homes.

NARCIS (Netherlands)

Achterberg, W.P.; Holtkamp, C.C.M.; Kerkstra, A.; Pot, A.M.; Ooms, M.E.; Ribbe, M.W.

2001-01-01

Aim: To study the effect of implementation of the Resident Assessment Instrument (RAI) on the quality of co-ordination of nursing care in Dutch nursing homes. Background: The Resident Assessment Instrument (RAI) was designed to improve the quality of care and quality of life in nursing homes. Until

Overstatement in happiness reporting with ordinal, bounded scale.

Science.gov (United States)

Tanaka, Saori C; Yamada, Katsunori; Kitada, Ryo; Tanaka, Satoshi; Sugawara, Sho K; Ohtake, Fumio; Sadato, Norihiro

2016-02-18

There are various methods by which people can express subjective evaluations quantitatively. For example, happiness can be measured on a scale from 1 to 10, and has been suggested as a measure of economic policy. However, there is resistance to these types of measurement from economists, who often regard welfare to be a cardinal, unbounded quantity. It is unclear whether there are differences between subjective evaluation reported on ordinal, bounded scales and on cardinal, unbounded scales. To answer this question, we developed functional magnetic resonance imaging experimental tasks for reporting happiness from monetary gain and the perception of visual stimulus. Subjects tended to report higher values when they used ordinal scales instead of cardinal scales. There were differences in neural activation between ordinal and cardinal reporting scales. The posterior parietal area showed greater activation when subjects used an ordinal scale instead of a cardinal scale. Importantly, the striatum exhibited greater activation when asked to report happiness on an ordinal scale than when asked to report on a cardinal scale. The finding that ordinal (bounded) scales are associated with higher reported happiness and greater activation in the reward system shows that overstatement bias in happiness data must be considered.

TAF6delta controls apoptosis and gene expression in the absence of p53.

Directory of Open Access Journals (Sweden)

Emmanuelle Wilhelm

Full Text Available BACKGROUND: Life and death decisions of metazoan cells hinge on the balance between the expression of pro- versus anti-apoptotic gene products. The general RNA polymerase II transcription factor, TFIID, plays a central role in the regulation of gene expression through its core promoter recognition and co-activator functions. The core TFIID subunit TAF6 acts in vitro as an essential co-activator of transcription for the p53 tumor suppressor protein. We previously identified a splice variant of TAF6, termed TAF6delta that can be induced during apoptosis. METHODOLOGY/PRINCIPAL FINDINGS: To elucidate the impact of TAF6delta on cell death and gene expression, we have employed modified antisense oligonucleotides to enforce expression of endogenous TAF6delta. The induction of endogenous TAF6delta triggered apoptosis in tumor cell lines, including cells devoid of p53. Microarray experiments revealed that TAF6delta activates gene expression independently of cellular p53 status. CONCLUSIONS: Our data define TAF6delta as a pivotal node in a signaling pathway that controls gene expression programs and apoptosis in the absence of p53.

Automated discovery of functional generality of human gene expression programs.

Directory of Open Access Journals (Sweden)

Georg K Gerber

2007-08-01

Full Text Available An important research problem in computational biology is the identification of expression programs, sets of co-expressed genes orchestrating normal or pathological processes, and the characterization of the functional breadth of these programs. The use of human expression data compendia for discovery of such programs presents several challenges including cellular inhomogeneity within samples, genetic and environmental variation across samples, uncertainty in the numbers of programs and sample populations, and temporal behavior. We developed GeneProgram, a new unsupervised computational framework based on Hierarchical Dirichlet Processes that addresses each of the above challenges. GeneProgram uses expression data to simultaneously organize tissues into groups and genes into overlapping programs with consistent temporal behavior, to produce maps of expression programs, which are sorted by generality scores that exploit the automatically learned groupings. Using synthetic and real gene expression data, we showed that GeneProgram outperformed several popular expression analysis methods. We applied GeneProgram to a compendium of 62 short time-series gene expression datasets exploring the responses of human cells to infectious agents and immune-modulating molecules. GeneProgram produced a map of 104 expression programs, a substantial number of which were significantly enriched for genes involved in key signaling pathways and/or bound by NF-kappaB transcription factors in genome-wide experiments. Further, GeneProgram discovered expression programs that appear to implicate surprising signaling pathways or receptor types in the response to infection, including Wnt signaling and neurotransmitter receptors. We believe the discovered map of expression programs involved in the response to infection will be useful for guiding future biological experiments; genes from programs with low generality scores might serve as new drug targets that exhibit minimal

Report on the consultants` meeting on co-ordination of the nuclear reaction data centers (technical aspects)

Energy Technology Data Exchange (ETDEWEB)

Schwerer, O; Wienke, H [eds.

1997-10-01

The report summarizes the co-ordination meeting of the network of Nuclear Reaction Data Centres organized by the IAEA in 1997. The meeting was attended by technical staff from ten member centres of the network (representing USA, Russia, China, Japan, Hungary, OECD-NEA and IAEA) to discuss technical matters of the nuclear data compilation and exchange by means of the jointly operated computerized systems CINDA, EXFOR, ENDF and others. Observers from Belgium and Ukraine also attended the meeting. The document includes status reports of all centres and selected working papers. Refs, figs, tabs.

Report on the consultants' meeting on co-ordination of the nuclear reaction data centers (technical aspects)

International Nuclear Information System (INIS)

Schwerer, O.; Wienke, H.

1997-10-01

The report summarizes the co-ordination meeting of the network of Nuclear Reaction Data Centres organized by the IAEA in 1997. The meeting was attended by technical staff from ten member centres of the network (representing USA, Russia, China, Japan, Hungary, OECD-NEA and IAEA) to discuss technical matters of the nuclear data compilation and exchange by means of the jointly operated computerized systems CINDA, EXFOR, ENDF and others. Observers from Belgium and Ukraine also attended the meeting. The document includes status reports of all centres and selected working papers

Evolutionary constraints shape caste-specific gene expression across 15 ant species.

Science.gov (United States)

Morandin, Claire; Mikheyev, Alexander S; Pedersen, Jes Søe; Helanterä, Heikki

2017-05-01

Development of polymorphic phenotypes from similar genomes requires gene expression differences. However, little is known about how morph-specific gene expression patterns vary on a broad phylogenetic scale. We hypothesize that evolution of morph-specific gene expression, and consequently morph-specific phenotypic evolution, may be constrained by gene essentiality and the amount of pleiotropic constraints. Here, we use comparative transcriptomics of queen and worker morphs, that is, castes, from 15 ant species to understand the constraints of morph-biased gene expression. In particular, we investigate how measures of evolutionary constraints at the sequence level (expression level, connectivity, and number of gene ontology [GO] terms) correlate with morph-biased expression. Our results show that genes indeed vary in their potential to become morph-biased. The existence of genes that are constrained in becoming caste-biased potentially limits the evolutionary decoupling of the caste phenotypes, that is, it might result in "caste load" occasioning from antagonistic fitness variation, similarly to sexually antagonistic fitness variation between males and females. On the other hand, we suggest that genes under low constraints are released from antagonistic variation and thus more likely to be co-opted for morph specific use. Overall, our results suggest that the factors that affect sequence evolutionary rates and evolution of plastic expression may largely overlap. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.