Gene expression, nucleotide composition and codon usage bias of genes associated with human Y chromosome.

Science.gov (United States)

Choudhury, Monisha Nath; Uddin, Arif; Chakraborty, Supriyo

2017-06-01

Analysis of codon usage pattern is important to understand the genetic and evolutionary characteristics of genomes. We have used bioinformatic approaches to analyze the codon usage bias (CUB) of the genes located in human Y chromosome. Codon bias index (CBI) indicated that the overall extent of codon usage bias was low. The relative synonymous codon usage (RSCU) analysis suggested that approximately half of the codons out of 59 synonymous codons were most frequently used, and possessed a T or G at the third codon position. The codon usage pattern was different in different genes as revealed from correspondence analysis (COA). A significant correlation between effective number of codons (ENC) and various GC contents suggests that both mutation pressure and natural selection affect the codon usage pattern of genes located in human Y chromosome. In addition, Y-linked genes have significant difference in GC contents at the second and third codon positions, expression level, and codon usage pattern of some codons like the SPANX genes in X chromosome.

Differential trends in the codon usage patterns in HIV-1 genes.

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Aridaman Pandit

Full Text Available Host-pathogen interactions underlie one of the most complex evolutionary phenomena resulting in continual adaptive genetic changes, where pathogens exploit the host's molecular resources for growth and survival, while hosts try to eliminate the pathogen. Deciphering the molecular basis of host-pathogen interactions is useful in understanding the factors governing pathogen evolution and disease propagation. In host-pathogen context, a balance between mutation, selection, and genetic drift is known to maintain codon bias in both organisms. Studies revealing determinants of the bias and its dynamics are central to the understanding of host-pathogen evolution. We considered the Human Immunodeficiency Virus (HIV type 1 and its human host to search for evolutionary signatures in the viral genome. Positive selection is known to dominate intra-host evolution of HIV-1, whereas high genetic variability underlies the belief that neutral processes drive inter-host differences. In this study, we analyze the codon usage patterns of HIV-1 genomes across all subtypes and clades sequenced over a period of 23 years. We show presence of unique temporal correlations in the codon bias of three HIV-1 genes illustrating differential adaptation of the HIV-1 genes towards the host preferred codons. Our results point towards gene-specific translational selection to be an important force driving the evolution of HIV-1 at the population level.

Codon usage and amino acid usage influence genes expression level.

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Paul, Prosenjit; Malakar, Arup Kumar; Chakraborty, Supriyo

2018-02-01

Highly expressed genes in any species differ in the usage frequency of synonymous codons. The relative recurrence of an event of the favored codon pair (amino acid pairs) varies between gene and genomes due to varying gene expression and different base composition. Here we propose a new measure for predicting the gene expression level, i.e., codon plus amino bias index (CABI). Our approach is based on the relative bias of the favored codon pair inclination among the genes, illustrated by analyzing the CABI score of the Medicago truncatula genes. CABI showed strong correlation with all other widely used measures (CAI, RCBS, SCUO) for gene expression analysis. Surprisingly, CABI outperforms all other measures by showing better correlation with the wet-lab data. This emphasizes the importance of the neighboring codons of the favored codon in a synonymous group while estimating the expression level of a gene.

Codon usage and expression level of human mitochondrial 13 protein coding genes across six continents.

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Chakraborty, Supriyo; Uddin, Arif; Mazumder, Tarikul Huda; Choudhury, Monisha Nath; Malakar, Arup Kumar; Paul, Prosenjit; Halder, Binata; Deka, Himangshu; Mazumder, Gulshana Akthar; Barbhuiya, Riazul Ahmed; Barbhuiya, Masuk Ahmed; Devi, Warepam Jesmi

2017-12-02

The study of codon usage coupled with phylogenetic analysis is an important tool to understand the genetic and evolutionary relationship of a gene. The 13 protein coding genes of human mitochondria are involved in electron transport chain for the generation of energy currency (ATP). However, no work has yet been reported on the codon usage of the mitochondrial protein coding genes across six continents. To understand the patterns of codon usage in mitochondrial genes across six different continents, we used bioinformatic analyses to analyze the protein coding genes. The codon usage bias was low as revealed from high ENC value. Correlation between codon usage and GC3 suggested that all the codons ending with G/C were positively correlated with GC3 but vice versa for A/T ending codons with the exception of ND4L and ND5 genes. Neutrality plot revealed that for the genes ATP6, COI, COIII, CYB, ND4 and ND4L, natural selection might have played a major role while mutation pressure might have played a dominant role in the codon usage bias of ATP8, COII, ND1, ND2, ND3, ND5 and ND6 genes. Phylogenetic analysis indicated that evolutionary relationships in each of 13 protein coding genes of human mitochondria were different across six continents and further suggested that geographical distance was an important factor for the origin and evolution of 13 protein coding genes of human mitochondria. Copyright © 2017 Elsevier B.V. and Mitochondria Research Society. All rights reserved.

Codon usage is associated with the evolutionary age of genes in metazoan genomes

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Linial Nathan

2009-12-01

Full Text Available Abstract Background Codon usage may vary significantly between different organisms and between genes within the same organism. Several evolutionary processes have been postulated to be the predominant determinants of codon usage: selection, mutation, and genetic drift. However, the relative contribution of each of these factors in different species remains debatable. The availability of complete genomes for tens of multicellular organisms provides an opportunity to inspect the relationship between codon usage and the evolutionary age of genes. Results We assign an evolutionary age to a gene based on the relative positions of its identified homologues in a standard phylogenetic tree. This yields a classification of all genes in a genome to several evolutionary age classes. The present study starts from the observation that each age class of genes has a unique codon usage and proceeds to provide a quantitative analysis of the codon usage in these classes. This observation is made for the genomes of Homo sapiens, Mus musculus, and Drosophila melanogaster. It is even more remarkable that the differences between codon usages in different age groups exhibit similar and consistent behavior in various organisms. While we find that GC content and gene length are also associated with the evolutionary age of genes, they can provide only a partial explanation for the observed codon usage. Conclusion While factors such as GC content, mutational bias, and selection shape the codon usage in a genome, the evolutionary history of an organism over hundreds of millions of years is an overlooked property that is strongly linked to GC content, protein length, and, even more significantly, to the codon usage of metazoan genomes.

Codon Usage Patterns of Tyrosinase Genes in Clonorchis sinensis.

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Bae, Young-An

2017-04-01

Codon usage bias (CUB) is a unique property of genomes and has contributed to the better understanding of the molecular features and the evolution processes of particular gene. In this study, genetic indices associated with CUB, including relative synonymous codon usage and effective numbers of codons, as well as the nucleotide composition, were investigated in the Clonorchis sinensis tyrosinase genes and their platyhelminth orthologs, which play an important role in the eggshell formation. The relative synonymous codon usage patterns substantially differed among tyrosinase genes examined. In a neutrality analysis, the correlation between GC 12 and GC 3 was statistically significant, and the regression line had a relatively gradual slope (0.218). NC-plot, i.e., GC 3 vs effective number of codons (ENC), showed that most of the tyrosinase genes were below the expected curve. The codon adaptation index (CAI) values of the platyhelminth tyrosinases had a narrow distribution between 0.685/0.714 and 0.797/0.837, and were negatively correlated with their ENC. Taken together, these results suggested that CUB in the tyrosinase genes seemed to be basically governed by selection pressures rather than mutational bias, although the latter factor provided an additional force in shaping CUB of the C. sinensis and Opisthorchis viverrini genes. It was also apparent that the equilibrium point between selection pressure and mutational bias is much more inclined to selection pressure in highly expressed C. sinensis genes, than in poorly expressed genes.

Genetic and codon usage bias analyses of polymerase genes of equine influenza virus and its relation to evolution.

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Bera, Bidhan Ch; Virmani, Nitin; Kumar, Naveen; Anand, Taruna; Pavulraj, S; Rash, Adam; Elton, Debra; Rash, Nicola; Bhatia, Sandeep; Sood, Richa; Singh, Raj Kumar; Tripathi, Bhupendra Nath

2017-08-23

Equine influenza is a major health problem of equines worldwide. The polymerase genes of influenza virus have key roles in virus replication, transcription, transmission between hosts and pathogenesis. Hence, the comprehensive genetic and codon usage bias of polymerase genes of equine influenza virus (EIV) were analyzed to elucidate the genetic and evolutionary relationships in a novel perspective. The group - specific consensus amino acid substitutions were identified in all polymerase genes of EIVs that led to divergence of EIVs into various clades. The consistent amino acid changes were also detected in the Florida clade 2 EIVs circulating in Europe and Asia since 2007. To study the codon usage patterns, a total of 281,324 codons of polymerase genes of EIV H3N8 isolates from 1963 to 2015 were systemically analyzed. The polymerase genes of EIVs exhibit a weak codon usage bias. The ENc-GC3s and Neutrality plots indicated that natural selection is the major influencing factor of codon usage bias, and that the impact of mutation pressure is comparatively minor. The methods for estimating host imposed translation pressure suggested that the polymerase acidic (PA) gene seems to be under less translational pressure compared to polymerase basic 1 (PB1) and polymerase basic 2 (PB2) genes. The multivariate statistical analysis of polymerase genes divided EIVs into four evolutionary diverged clusters - Pre-divergent, Eurasian, Florida sub-lineage 1 and 2. Various lineage specific amino acid substitutions observed in all polymerase genes of EIVs and especially, clade 2 EIVs underwent major variations which led to the emergence of a phylogenetically distinct group of EIVs originating from Richmond/1/07. The codon usage bias was low in all the polymerase genes of EIVs that was influenced by the multiple factors such as the nucleotide compositions, mutation pressure, aromaticity and hydropathicity. However, natural selection was the major influencing factor in defining the

Biased immunoglobulin light chain gene usage in the shark1

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Iacoangeli, Anna; Lui, Anita; Naik, Ushma; Ohta, Yuko; Flajnik, Martin; Hsu, Ellen

2015-01-01

This study of a large family of kappa light (L) chain clusters in nurse shark completes the characterization of its classical immunoglobulin (Ig) gene content (two heavy chain classes, mu and omega, and four L chain isotopes, kappa, lambda, sigma, and sigma-2). The shark kappa clusters are minigenes consisting of a simple VL-JL-CL array, where V to J recombination occurs over a ~500 bp interval, and functional clusters are widely separated by at least 100 kb. Six out of ca. 39 kappa clusters are pre-rearranged in the germline (GL-joined). Unlike the complex gene organization and multistep assembly process of Ig in mammals, each shark Ig rearrangement, somatic or in the germline, appears to be an independent event localized to the minigene. This study examined the expression of functional, non-productive, and sterile transcripts of the kappa clusters compared to the other three L chain isotypes. Kappa cluster usage was investigated in young sharks, and a skewed pattern of split gene expression was observed, one similar in functional and non-productive rearrangements. These results show that the individual activation of the spatially distant kappa clusters is non-random. Although both split and GL-joined kappa genes are expressed, the latter are prominent in young animals and wane with age. We speculate that, in the shark, the differential activation of the multiple isotypes can be advantageously used in receptor editing. PMID:26342033

Gaining insights into the codon usage patterns of TP53 gene across eight mammalian species.

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Tarikul Huda Mazumder

Full Text Available TP53 gene is known as the "guardian of the genome" as it plays a vital role in regulating cell cycle, cell proliferation, DNA damage repair, initiation of programmed cell death and suppressing tumor growth. Non uniform usage of synonymous codons for a specific amino acid during translation of protein known as codon usage bias (CUB is a unique property of the genome and shows species specific deviation. Analysis of codon usage bias with compositional dynamics of coding sequences has contributed to the better understanding of the molecular mechanism and the evolution of a particular gene. In this study, the complete nucleotide coding sequences of TP53 gene from eight different mammalian species were used for CUB analysis. Our results showed that the codon usage patterns in TP53 gene across different mammalian species has been influenced by GC bias particularly GC3 and a moderate bias exists in the codon usage of TP53 gene. Moreover, we observed that nature has highly favored the most over represented codon CTG for leucine amino acid but selected against the ATA codon for isoleucine in TP53 gene across all mammalian species during the course of evolution.

Codon usage bias and the evolution of influenza A viruses. Codon Usage Biases of Influenza Virus

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Wong Emily HM

2010-08-01

Full Text Available Abstract Background The influenza A virus is an important infectious cause of morbidity and mortality in humans and was responsible for 3 pandemics in the 20th century. As the replication of the influenza virus is based on its host's machinery, codon usage of its viral genes might be subject to host selection pressures, especially after interspecies transmission. A better understanding of viral evolution and host adaptive responses might help control this disease. Results Relative Synonymous Codon Usage (RSCU values of the genes from segment 1 to segment 6 of avian and human influenza viruses, including pandemic H1N1, were studied via Correspondence Analysis (CA. The codon usage patterns of seasonal human influenza viruses were distinct among their subtypes and different from those of avian viruses. Newly isolated viruses could be added to the CA results, creating a tool to investigate the host origin and evolution of viral genes. It was found that the 1918 pandemic H1N1 virus contained genes with mammalian-like viral codon usage patterns, indicating that the introduction of this virus to humans was not through in toto transfer of an avian influenza virus. Many human viral genes had directional changes in codon usage over time of viral isolation, indicating the effect of host selection pressures. These changes reduced the overall GC content and the usage of G at the third codon position in the viral genome. Limited evidence of translational selection pressure was found in a few viral genes. Conclusions Codon usage patterns from CA allowed identification of host origin and evolutionary trends in influenza viruses, providing an alternative method and a tool to understand the evolution of influenza viruses. Human influenza viruses are subject to selection pressure on codon usage which might assist in understanding the characteristics of newly emerging viruses.

HIV1 V3 loop hypermutability is enhanced by the guanine usage bias in the part of env gene coding for it.

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Khrustalev, Vladislav Victorovich

2009-01-01

Guanine is the most mutable nucleotide in HIV genes because of frequently occurring G to A transitions, which are caused by cytosine deamination in viral DNA minus strands catalyzed by APOBEC enzymes. Distribution of guanine between three codon positions should influence the probability for G to A mutation to be nonsynonymous (to occur in first or second codon position). We discovered that nucleotide sequences of env genes coding for third variable regions (V3 loops) of gp120 from HIV1 and HIV2 have different kinds of guanine usage biases. In the HIV1 reference strain and 100 additionally analyzed HIV1 strains the guanine usage bias in V3 loop coding regions (2G>1G>3G) should lead to elevated nonsynonymous G to A transitions occurrence rates. In the HIV2 reference strain and 100 other HIV2 strains guanine usage bias in V3 loop coding regions (3G>2G>1G) should protect V3 loops from hypermutability. According to the HIV1 and HIV2 V3 alignment, insertion of the sequence enriched with 2G (21 codons in length) occurred during the evolution of HIV1 predecessor, while insertion of the different sequence enriched with 3G (19 codons in length) occurred during the evolution of HIV2 predecessor. The higher is the level of 3G in the V3 coding region, the lower should be the immune escaping mutation occurrence rates. This hypothesis was tested in this study by comparing the guanine usage in V3 loop coding regions from HIV1 fast and slow progressors. All calculations have been performed by our algorithms "VVK In length", "VVK Dinucleotides" and "VVK Consensus" (www.barkovsky.hotmail.ru).

Gene-wide analysis detects two new susceptibility genes for Alzheimer's disease.

Science.gov (United States)

Escott-Price, Valentina; Bellenguez, Céline; Wang, Li-San; Choi, Seung-Hoan; Harold, Denise; Jones, Lesley; Holmans, Peter; Gerrish, Amy; Vedernikov, Alexey; Richards, Alexander; DeStefano, Anita L; Lambert, Jean-Charles; Ibrahim-Verbaas, Carla A; Naj, Adam C; Sims, Rebecca; Jun, Gyungah; Bis, Joshua C; Beecham, Gary W; Grenier-Boley, Benjamin; Russo, Giancarlo; Thornton-Wells, Tricia A; Denning, Nicola; Smith, Albert V; Chouraki, Vincent; Thomas, Charlene; Ikram, M Arfan; Zelenika, Diana; Vardarajan, Badri N; Kamatani, Yoichiro; Lin, Chiao-Feng; Schmidt, Helena; Kunkle, Brian; Dunstan, Melanie L; Vronskaya, Maria; Johnson, Andrew D; Ruiz, Agustin; Bihoreau, Marie-Thérèse; Reitz, Christiane; Pasquier, Florence; Hollingworth, Paul; Hanon, Olivier; Fitzpatrick, Annette L; Buxbaum, Joseph D; Campion, Dominique; Crane, Paul K; Baldwin, Clinton; Becker, Tim; Gudnason, Vilmundur; Cruchaga, Carlos; Craig, David; Amin, Najaf; Berr, Claudine; Lopez, Oscar L; De Jager, Philip L; Deramecourt, Vincent; Johnston, Janet A; Evans, Denis; Lovestone, Simon; Letenneur, Luc; Hernández, Isabel; Rubinsztein, David C; Eiriksdottir, Gudny; Sleegers, Kristel; Goate, Alison M; Fiévet, Nathalie; Huentelman, Matthew J; Gill, Michael; Brown, Kristelle; Kamboh, M Ilyas; Keller, Lina; Barberger-Gateau, Pascale; McGuinness, Bernadette; Larson, Eric B; Myers, Amanda J; Dufouil, Carole; Todd, Stephen; Wallon, David; Love, Seth; Rogaeva, Ekaterina; Gallacher, John; George-Hyslop, Peter St; Clarimon, Jordi; Lleo, Alberto; Bayer, Anthony; Tsuang, Debby W; Yu, Lei; Tsolaki, Magda; Bossù, Paola; Spalletta, Gianfranco; Proitsi, Petra; Collinge, John; Sorbi, Sandro; Garcia, Florentino Sanchez; Fox, Nick C; Hardy, John; Naranjo, Maria Candida Deniz; Bosco, Paolo; Clarke, Robert; Brayne, Carol; Galimberti, Daniela; Scarpini, Elio; Bonuccelli, Ubaldo; Mancuso, Michelangelo; Siciliano, Gabriele; Moebus, Susanne; Mecocci, Patrizia; Zompo, Maria Del; Maier, Wolfgang; Hampel, Harald; Pilotto, Alberto; Frank-García, Ana; Panza, Francesco; Solfrizzi, Vincenzo; Caffarra, Paolo; Nacmias, Benedetta; Perry, William; Mayhaus, Manuel; Lannfelt, Lars; Hakonarson, Hakon; Pichler, Sabrina; Carrasquillo, Minerva M; Ingelsson, Martin; Beekly, Duane; Alvarez, Victoria; Zou, Fanggeng; Valladares, Otto; Younkin, Steven G; Coto, Eliecer; Hamilton-Nelson, Kara L; Gu, Wei; Razquin, Cristina; Pastor, Pau; Mateo, Ignacio; Owen, Michael J; Faber, Kelley M; Jonsson, Palmi V; Combarros, Onofre; O'Donovan, Michael C; Cantwell, Laura B; Soininen, Hilkka; Blacker, Deborah; Mead, Simon; Mosley, Thomas H; Bennett, David A; Harris, Tamara B; Fratiglioni, Laura; Holmes, Clive; de Bruijn, Renee F A G; Passmore, Peter; Montine, Thomas J; Bettens, Karolien; Rotter, Jerome I; Brice, Alexis; Morgan, Kevin; Foroud, Tatiana M; Kukull, Walter A; Hannequin, Didier; Powell, John F; Nalls, Michael A; Ritchie, Karen; Lunetta, Kathryn L; Kauwe, John S K; Boerwinkle, Eric; Riemenschneider, Matthias; Boada, Mercè; Hiltunen, Mikko; Martin, Eden R; Schmidt, Reinhold; Rujescu, Dan; Dartigues, Jean-François; Mayeux, Richard; Tzourio, Christophe; Hofman, Albert; Nöthen, Markus M; Graff, Caroline; Psaty, Bruce M; Haines, Jonathan L; Lathrop, Mark; Pericak-Vance, Margaret A; Launer, Lenore J; Van Broeckhoven, Christine; Farrer, Lindsay A; van Duijn, Cornelia M; Ramirez, Alfredo; Seshadri, Sudha; Schellenberg, Gerard D; Amouyel, Philippe; Williams, Julie

2014-01-01

Alzheimer's disease is a common debilitating dementia with known heritability, for which 20 late onset susceptibility loci have been identified, but more remain to be discovered. This study sought to identify new susceptibility genes, using an alternative gene-wide analytical approach which tests for patterns of association within genes, in the powerful genome-wide association dataset of the International Genomics of Alzheimer's Project Consortium, comprising over 7 m genotypes from 25,580 Alzheimer's cases and 48,466 controls. In addition to earlier reported genes, we detected genome-wide significant loci on chromosomes 8 (TP53INP1, p = 1.4×10-6) and 14 (IGHV1-67 p = 7.9×10-8) which indexed novel susceptibility loci. The additional genes identified in this study, have an array of functions previously implicated in Alzheimer's disease, including aspects of energy metabolism, protein degradation and the immune system and add further weight to these pathways as potential therapeutic targets in Alzheimer's disease.

Gene-wide analysis detects two new susceptibility genes for Alzheimer's disease.

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Valentina Escott-Price

Full Text Available Alzheimer's disease is a common debilitating dementia with known heritability, for which 20 late onset susceptibility loci have been identified, but more remain to be discovered. This study sought to identify new susceptibility genes, using an alternative gene-wide analytical approach which tests for patterns of association within genes, in the powerful genome-wide association dataset of the International Genomics of Alzheimer's Project Consortium, comprising over 7 m genotypes from 25,580 Alzheimer's cases and 48,466 controls.In addition to earlier reported genes, we detected genome-wide significant loci on chromosomes 8 (TP53INP1, p = 1.4×10-6 and 14 (IGHV1-67 p = 7.9×10-8 which indexed novel susceptibility loci.The additional genes identified in this study, have an array of functions previously implicated in Alzheimer's disease, including aspects of energy metabolism, protein degradation and the immune system and add further weight to these pathways as potential therapeutic targets in Alzheimer's disease.

Regional differences in gene expression and promoter usage in aged human brains

KAUST Repository

Pardo, Luba M.

2013-02-19

To characterize the promoterome of caudate and putamen regions (striatum), frontal and temporal cortices, and hippocampi from aged human brains, we used high-throughput cap analysis of gene expression to profile the transcription start sites and to quantify the differences in gene expression across the 5 brain regions. We also analyzed the extent to which methylation influenced the observed expression profiles. We sequenced more than 71 million cap analysis of gene expression tags corresponding to 70,202 promoter regions and 16,888 genes. More than 7000 transcripts were differentially expressed, mainly because of differential alternative promoter usage. Unexpectedly, 7% of differentially expressed genes were neurodevelopmental transcription factors. Functional pathway analysis on the differentially expressed genes revealed an overrepresentation of several signaling pathways (e.g., fibroblast growth factor and wnt signaling) in hippocampus and striatum. We also found that although 73% of methylation signals mapped within genes, the influence of methylation on the expression profile was small. Our study underscores alternative promoter usage as an important mechanism for determining the regional differences in gene expression at old age.

Comparative analysis of codon usage patterns and identification of predicted highly expressed genes in five Salmonella genomes

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Mondal U

2008-01-01

Full Text Available Purpose: To anlyse codon usage patterns of five complete genomes of Salmonella , predict highly expressed genes, examine horizontally transferred pathogenicity-related genes to detect their presence in the strains, and scrutinize the nature of highly expressed genes to infer upon their lifestyle. Methods: Protein coding genes, ribosomal protein genes, and pathogenicity-related genes were analysed with Codon W and CAI (codon adaptation index Calculator. Results: Translational efficiency plays a role in codon usage variation in Salmonella genes. Low bias was noticed in most of the genes. GC3 (guanine cytosine at third position composition does not influence codon usage variation in the genes of these Salmonella strains. Among the cluster of orthologous groups (COGs, translation, ribosomal structure biogenesis [J], and energy production and conversion [C] contained the highest number of potentially highly expressed (PHX genes. Correspondence analysis reveals the conserved nature of the genes. Highly expressed genes were detected. Conclusions: Selection for translational efficiency is the major source of variation of codon usage in the genes of Salmonella . Evolution of pathogenicity-related genes as a unit suggests their ability to infect and exist as a pathogen. Presence of a lot of PHX genes in the information and storage-processing category of COGs indicated their lifestyle and revealed that they were not subjected to genome reduction.

ABCA1 C69T gene polymorphism and risk of type 2 diabetes ...

Indian Academy of Sciences (India)

2013-11-06

Nov 6, 2013 ... especially in high-density lipoprotein cholesterol (HDL-C). (Daimona et al. 2005 ... glucose, triglyceride (TG), total cholesterol (TC) and HDL-C levels were ... relationship between ABCA1 C69T genotypes and lipid profiles was ...

Intraclonal Cell Expansion and Selection Driven by B Cell Receptor in Chronic Lymphocytic Leukemia

Science.gov (United States)

Colombo, Monica; Cutrona, Giovanna; Reverberi, Daniele; Fabris, Sonia; Neri, Antonino; Fabbi, Marina; Quintana, Giovanni; Quarta, Giovanni; Ghiotto, Fabio; Fais, Franco; Ferrarini, Manlio

2011-01-01

The mutational status of the immunoglobulin heavy-chain variable region (IGHV) genes utilized by chronic lymphocytic leukemia (CLL) clones defines two disease subgroups. Patients with unmutated IGHV have a more aggressive disease and a worse outcome than patients with cells having somatic IGHV gene mutations. Moreover, up to 30% of the unmutated CLL clones exhibit very similar or identical B cell receptors (BcR), often encoded by the same IG genes. These “stereotyped” BcRs have been classified into defined subsets. The presence of an IGHV gene somatic mutation and the utilization of a skewed gene repertoire compared with normal B cells together with the expression of stereotyped receptors by unmutated CLL clones may indicate stimulation/selection by antigenic epitopes. This antigenic stimulation may occur prior to or during neoplastic transformation, but it is unknown whether this stimulation/selection continues after leukemogenesis has ceased. In this study, we focused on seven CLL cases with stereotyped BcR Subset #8 found among a cohort of 700 patients; in six, the cells expressed IgG and utilized IGHV4-39 and IGKV1-39/IGKV1D-39 genes, as reported for Subset #8 BcR. One case exhibited special features, including expression of IgM or IgG by different subclones consequent to an isotype switch, allelic inclusion at the IGH locus in the IgM-expressing cells and a particular pattern of cytogenetic lesions. Collectively, the data indicate a process of antigenic stimulation/selection of the fully transformed CLL cells leading to the expansion of the Subset #8 IgG-bearing subclone. PMID:21541442

Gene cluster analysis for the biosynthesis of elgicins, novel lantibiotics produced by paenibacillus elgii B69

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Teng Yi

2012-03-01

Full Text Available Abstract Background The recent increase in bacterial resistance to antibiotics has promoted the exploration of novel antibacterial materials. As a result, many researchers are undertaking work to identify new lantibiotics because of their potent antimicrobial activities. The objective of this study was to provide details of a lantibiotic-like gene cluster in Paenibacillus elgii B69 and to produce the antibacterial substances coded by this gene cluster based on culture screening. Results Analysis of the P. elgii B69 genome sequence revealed the presence of a lantibiotic-like gene cluster composed of five open reading frames (elgT1, elgC, elgT2, elgB, and elgA. Screening of culture extracts for active substances possessing the predicted properties of the encoded product led to the isolation of four novel peptides (elgicins AI, AII, B, and C with a broad inhibitory spectrum. The molecular weights of these peptides were 4536, 4593, 4706, and 4820 Da, respectively. The N-terminal sequence of elgicin B was Leu-Gly-Asp-Tyr, which corresponded to the partial sequence of the peptide ElgA encoded by elgA. Edman degradation suggested that the product elgicin B is derived from ElgA. By correlating the results of electrospray ionization-mass spectrometry analyses of elgicins AI, AII, and C, these peptides are deduced to have originated from the same precursor, ElgA. Conclusions A novel lantibiotic-like gene cluster was shown to be present in P. elgii B69. Four new lantibiotics with a broad inhibitory spectrum were isolated, and these appear to be promising antibacterial agents.

Local synteny and codon usage contribute to asymmetric sequence divergence of Saccharomyces cerevisiae gene duplicates

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Bergthorsson Ulfar

2011-09-01

Full Text Available Abstract Background Duplicated genes frequently experience asymmetric rates of sequence evolution. Relaxed selective constraints and positive selection have both been invoked to explain the observation that one paralog within a gene-duplicate pair exhibits an accelerated rate of sequence evolution. In the majority of studies where asymmetric divergence has been established, there is no indication as to which gene copy, ancestral or derived, is evolving more rapidly. In this study we investigated the effect of local synteny (gene-neighborhood conservation and codon usage on the sequence evolution of gene duplicates in the S. cerevisiae genome. We further distinguish the gene duplicates into those that originated from a whole-genome duplication (WGD event (ohnologs versus small-scale duplications (SSD to determine if there exist any differences in their patterns of sequence evolution. Results For SSD pairs, the derived copy evolves faster than the ancestral copy. However, there is no relationship between rate asymmetry and synteny conservation (ancestral-like versus derived-like in ohnologs. mRNA abundance and optimal codon usage as measured by the CAI is lower in the derived SSD copies relative to ancestral paralogs. Moreover, in the case of ohnologs, the faster-evolving copy has lower CAI and lowered expression. Conclusions Together, these results suggest that relaxation of selection for codon usage and gene expression contribute to rate asymmetry in the evolution of duplicated genes and that in SSD pairs, the relaxation of selection stems from the loss of ancestral regulatory information in the derived copy.

Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels

DEFF Research Database (Denmark)

Frenkel-Morgenstern, Milana; Danon, Tamar; Christian, Thomas

2012-01-01

The cell cycle is a temporal program that regulates DNA synthesis and cell division. When we compared the codon usage of cell cycle-regulated genes with that of other genes, we discovered that there is a significant preference for non-optimal codons. Moreover, genes encoding proteins that cycle a...

Loss of the BMP antagonist USAG-1 ameliorates disease in a mouse model of the progressive hereditary kidney disease Alport syndrome.

Science.gov (United States)

Tanaka, Mari; Asada, Misako; Higashi, Atsuko Y; Nakamura, Jin; Oguchi, Akiko; Tomita, Mayumi; Yamada, Sachiko; Asada, Nariaki; Takase, Masayuki; Okuda, Tomohiko; Kawachi, Hiroshi; Economides, Aris N; Robertson, Elizabeth; Takahashi, Satoru; Sakurai, Takeshi; Goldschmeding, Roel; Muso, Eri; Fukatsu, Atsushi; Kita, Toru; Yanagita, Motoko

2010-03-01

The glomerular basement membrane (GBM) is a key component of the filtering unit in the kidney. Mutations involving any of the collagen IV genes (COL4A3, COL4A4, and COL4A5) affect GBM assembly and cause Alport syndrome, a progressive hereditary kidney disease with no definitive therapy. Previously, we have demonstrated that the bone morphogenetic protein (BMP) antagonist uterine sensitization-associated gene-1 (USAG-1) negatively regulates the renoprotective action of BMP-7 in a mouse model of tubular injury during acute renal failure. Here, we investigated the role of USAG-1 in renal function in Col4a3-/- mice, which model Alport syndrome. Ablation of Usag1 in Col4a3-/- mice led to substantial attenuation of disease progression, normalization of GBM ultrastructure, preservation of renal function, and extension of life span. Immunohistochemical analysis revealed that USAG-1 and BMP-7 colocalized in the macula densa in the distal tubules, lying in direct contact with glomerular mesangial cells. Furthermore, in cultured mesangial cells, BMP-7 attenuated and USAG-1 enhanced the expression of MMP-12, a protease that may contribute to GBM degradation. These data suggest that the pathogenetic role of USAG-1 in Col4a3-/- mice might involve crosstalk between kidney tubules and the glomerulus and that inhibition of USAG-1 may be a promising therapeutic approach for the treatment of Alport syndrome.

Separate base usages of genes located on the leading and lagging strands in Chlamydia muridarum revealed by the Z curve method

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Yu Xiu-Juan

2007-10-01

Full Text Available Abstract Background The nucleotide compositional asymmetry between the leading and lagging strands in bacterial genomes has been the subject of intensive study in the past few years. It is interesting to mention that almost all bacterial genomes exhibit the same kind of base asymmetry. This work aims to investigate the strand biases in Chlamydia muridarum genome and show the potential of the Z curve method for quantitatively differentiating genes on the leading and lagging strands. Results The occurrence frequencies of bases of protein-coding genes in C. muridarum genome were analyzed by the Z curve method. It was found that genes located on the two strands of replication have distinct base usages in C. muridarum genome. According to their positions in the 9-D space spanned by the variables u1 – u9 of the Z curve method, K-means clustering algorithm can assign about 94% of genes to the correct strands, which is a few percent higher than those correctly classified by K-means based on the RSCU. The base usage and codon usage analyses show that genes on the leading strand have more G than C and more T than A, particularly at the third codon position. For genes on the lagging strand the biases is reverse. The y component of the Z curves for the complete chromosome sequences show that the excess of G over C and T over A are more remarkable in C. muridarum genome than in other bacterial genomes without separating base and/or codon usages. Furthermore, for the genomes of Borrelia burgdorferi, Treponema pallidum, Chlamydia muridarum and Chlamydia trachomatis, in which distinct base and/or codon usages have been observed, closer phylogenetic distance is found compared with other bacterial genomes. Conclusion The nature of the strand biases of base composition in C. muridarum is similar to that in most other bacterial genomes. However, the base composition asymmetry between the leading and lagging strands in C. muridarum is more significant than that in

Quantitative Analysis of Repertoire-Scale Immunoglobulin Properties in Vaccine-Induced B-Cell Responses

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Ilja V. Khavrutskii

2017-08-01

Full Text Available Recent advances in the next-generation sequencing of B-cell receptors (BCRs enable the characterization of humoral responses at a repertoire-wide scale and provide the capability for identifying unique features of immune repertoires in response to disease, vaccination, or infection. Immunosequencing now readily generates 103–105 sequences per sample; however, statistical analysis of these repertoires is challenging because of the high genetic diversity of BCRs and the elaborate clonal relationships among them. To date, most immunosequencing analyses have focused on reporting qualitative trends in immunoglobulin (Ig properties, such as usage or somatic hypermutation (SHM percentage of the Ig heavy chain variable (IGHV gene segment family, and on reducing complex Ig property distributions to simple summary statistics. However, because Ig properties are typically not normally distributed, any approach that fails to assess the distribution as a whole may be inadequate in (1 properly assessing the statistical significance of repertoire differences, (2 identifying how two repertoires differ, and (3 determining appropriate confidence intervals for assessing the size of the differences and their potential biological relevance. To address these issues, we have developed a technique that uses Wilcox’ robust statistics toolbox to identify statistically significant vaccine-specific differences between Ig repertoire properties. The advantage of this technique is that it can determine not only whether but also where the distributions differ, even when the Ig repertoire properties are non-normally distributed. We used this technique to characterize murine germinal center (GC B-cell repertoires in response to a complex Ebola virus-like particle (eVLP vaccine candidate with known protective efficacy. The eVLP-mediated GC B-cell responses were highly diverse, consisting of thousands of clonotypes. Despite this staggering diversity, we identified statistically

High-throughput sequencing of the B-cell receptor in African Burkitt lymphoma reveals clues to pathogenesis.

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Lombardo, Katharine A; Coffey, David G; Morales, Alicia J; Carlson, Christopher S; Towlerton, Andrea M H; Gerdts, Sarah E; Nkrumah, Francis K; Neequaye, Janet; Biggar, Robert J; Orem, Jackson; Casper, Corey; Mbulaiteye, Sam M; Bhatia, Kishor G; Warren, Edus H

2017-03-28

Burkitt lymphoma (BL), the most common pediatric cancer in sub-Saharan Africa, is a malignancy of antigen-experienced B lymphocytes. High-throughput sequencing (HTS) of the immunoglobulin heavy ( IGH ) and light chain ( IGK / IGL ) loci was performed on genomic DNA from 51 primary BL tumors: 19 from Uganda and 32 from Ghana. Reverse transcription polymerase chain reaction analysis and tumor RNA sequencing (RNAseq) was performed on the Ugandan tumors to confirm and extend the findings from the HTS of tumor DNA. Clonal IGH and IGK / IGL rearrangements were identified in 41 and 46 tumors, respectively. Evidence for rearrangement of the second IGH allele was observed in only 6 of 41 tumor samples with a clonal IGH rearrangement, suggesting that the normal process of biallelic IGHD to IGHJ diversity-joining (DJ) rearrangement is often disrupted in BL progenitor cells. Most tumors, including those with a sole dominant, nonexpressed DJ rearrangement, contained many IGH and IGK / IGL sequences that differed from the dominant rearrangement by < 10 nucleotides, suggesting that the target of ongoing mutagenesis of these loci in BL tumor cells is not limited to expressed alleles. IGHV usage in both BL tumor cohorts revealed enrichment for IGHV genes that are infrequently used in memory B cells from healthy subjects. Analysis of publicly available DNA sequencing and RNAseq data revealed that these same IGHV genes were overrepresented in dominant tumor-associated IGH rearrangements in several independent BL tumor cohorts. These data suggest that BL derives from an abnormal B-cell progenitor and that aberrant mutational processes are active on the immunoglobulin loci in BL cells.

Mutation Pattern of Paired Immunoglobulin Heavy and Light Variable Domains in Chronic Lymphocytic Leukemia B Cells

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Ghiotto, Fabio; Marcatili, Paolo

2011-01-01

B-cell chronic lymphocytic leukemia (CLL) patients display leukemic clones bearing either germline or somatically mutated immunoglobulin heavy variable (IGHV ) genes. Most information on CLL immunoglobulins (Igs), such as the definition of stereotyped B-cell receptors (BCRs), was derived from germline unmutated Igs. In particular, detailed studies on the distribution and nature of mutations in paired heavy- and light-chain domains of CLL clones bearing mutated Igs are lacking. To address the somatic hyper-mutation dynamics of CLL Igs, we analyzed the mutation pattern of paired IGHV-diversity-joining (IGHV-D-J ) and immunoglobulin kappa/lambda variable-joining (IGK/LV-J ) rearrangements of 193 leukemic clones that displayed ≥ 2% mutations in at least one of the two immunoglobulin variable (IGV ) genes (IGHV and/or IGK/LV ). The relationship between the mutation frequency in IGHV and IGK/LV complementarity determining regions (CDRs) and framework regions (FRs) was evaluated by correlation analysis. Replacement (R) mutation frequency within IGK/LV chain CDRs correlated significantly with mutation frequency of paired IGHV CDRs in λ but not κ isotype CLL clones. CDRs of IGKV-J rearrangements displayed a lower percentage of R mutations than IGHVs. The frequency/pattern of mutations in kappa CLL Igs differed also from that in κ-expressing normal B cells described in the literature. Instead, the mutation frequency within the FRs of IGHV and either IGKV or IGLV was correlated. Notably, the amount of diversity introduced by replaced amino acids was comparable between IGHVs and IGKVs. The data indicate a different mutation pattern between κ and λ isotype CLL clones and suggest an antigenic selection that, in κ samples, operates against CDR variation.

Data on genome analysis of Bacillus velezensis LS69.

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Liu, Guoqiang; Kong, Yingying; Fan, Yajing; Geng, Ce; Peng, Donghai; Sun, Ming

2017-08-01

The data presented in this article are related to the published entitled "Whole-genome sequencing of Bacillus velezensis LS69, a strain with a broad inhibitory spectrum against pathogenic bacteria" (Liu et al., 2017) [1]. Genome analysis revealed B. velezensis LS69 has a good potential for biocontrol and plant growth promotion. This article provides an extended analysis of the genetic islands, core genes and amylolysin loci of B. velezensis LS69.

Data on genome analysis of Bacillus velezensis LS69

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Liu, Guoqiang; Kong, Yingying; Fan, Yajing; Geng, Ce; Peng, Donghai; Sun, Ming

2017-01-01

The data presented in this article are related to the published entitled “Whole-genome sequencing of Bacillus velezensis LS69, a strain with a broad inhibitory spectrum against pathogenic bacteria” (Liu et al., 2017) [1]. Genome analysis revealed B. velezensis LS69 has a good potential for biocontrol and plant growth promotion. This article provides an extended analysis of the genetic islands, core genes and amylolysin loci of B. velezensis LS69.

Insight into pattern of codon biasness and nucleotide base usage in serotonin receptor gene family from different mammalian species.

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Dass, J Febin Prabhu; Sudandiradoss, C

2012-07-15

5-HT (5-Hydroxy-tryptamine) or serotonin receptors are found both in central and peripheral nervous system as well as in non-neuronal tissues. In the animal and human nervous system, serotonin produces various functional effects through a variety of membrane bound receptors. In this study, we focus on 5-HT receptor family from different mammals and examined the factors that account for codon and nucleotide usage variation. A total of 110 homologous coding sequences from 11 different mammalian species were analyzed using relative synonymous codon usage (RSCU), correspondence analysis (COA) and hierarchical cluster analysis together with nucleotide base usage frequency of chemically similar amino acid codons. The mean effective number of codon (ENc) value of 37.06 for 5-HT(6) shows very high codon bias within the family and may be due to high selective translational efficiency. The COA and Spearman's rank correlation reveals that the nucleotide compositional mutation bias as the major factors influencing the codon usage in serotonin receptor genes. The hierarchical cluster analysis suggests that gene function is another dominant factor that affects the codon usage bias, while species is a minor factor. Nucleotide base usage was reported using Goldman, Engelman, Stietz (GES) scale reveals the presence of high uracil (>45%) content at functionally important hydrophobic regions. Our in silico approach will certainly help for further investigations on critical inference on evolution, structure, function and gene expression aspects of 5-HT receptors family which are potential antipsychotic drug targets. Copyright © 2012 Elsevier B.V. All rights reserved.

Complex Codon Usage Pattern and Compositional Features of Retroviruses

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Sourav RoyChoudhury

2013-01-01

Full Text Available Retroviruses infect a wide range of organisms including humans. Among them, HIV-1, which causes AIDS, has now become a major threat for world health. Some of these viruses are also potential gene transfer vectors. In this study, the patterns of synonymous codon usage in retroviruses have been studied through multivariate statistical methods on ORFs sequences from the available 56 retroviruses. The principal determinant for evolution of the codon usage pattern in retroviruses seemed to be the compositional constraints, while selection for translation of the viral genes plays a secondary role. This was further supported by multivariate analysis on relative synonymous codon usage. Thus, it seems that mutational bias might have dominated role over translational selection in shaping the codon usage of retroviruses. Codon adaptation index was used to identify translationally optimal codons among genes from retroviruses. The comparative analysis of the preferred and optimal codons among different retroviral groups revealed that four codons GAA, AAA, AGA, and GGA were significantly more frequent in most of the retroviral genes inspite of some differences. Cluster analysis also revealed that phylogenetically related groups of retroviruses have probably evolved their codon usage in a concerted manner under the influence of their nucleotide composition.

Data on genome analysis of Bacillus velezensis LS69

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Guoqiang Liu

2017-08-01

Full Text Available The data presented in this article are related to the published entitled “Whole-genome sequencing of Bacillus velezensis LS69, a strain with a broad inhibitory spectrum against pathogenic bacteria” (Liu et al., 2017 [1]. Genome analysis revealed B. velezensis LS69 has a good potential for biocontrol and plant growth promotion. This article provides an extended analysis of the genetic islands, core genes and amylolysin loci of B. velezensis LS69.

Analysis of phylogeny and codon usage bias and relationship of GC content, amino acid composition with expression of the structural nif genes.

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Mondal, Sunil Kanti; Kundu, Sudip; Das, Rabindranath; Roy, Sujit

2016-08-01

Bacteria and archaea have evolved with the ability to fix atmospheric dinitrogen in the form of ammonia, catalyzed by the nitrogenase enzyme complex which comprises three structural genes nifK, nifD and nifH. The nifK and nifD encodes for the beta and alpha subunits, respectively, of component 1, while nifH encodes for component 2 of nitrogenase. Phylogeny based on nifDHK have indicated that Cyanobacteria is closer to Proteobacteria alpha and gamma but not supported by the tree based on 16SrRNA. The evolutionary ancestor for the different trees was also different. The GC1 and GC2% analysis showed more consistency than GC3% which appeared to below for Firmicutes, Cyanobacteria and Euarchaeota while highest in Proteobacteria beta and clearly showed the proportional effect on the codon usage with a few exceptions. Few genes from Firmicutes, Euryarchaeota, Proteobacteria alpha and delta were found under mutational pressure. These nif genes with low and high GC3% from different classes of organisms showed similar expected number of codons. Distribution of the genes and codons, based on codon usage demonstrated opposite pattern for different orientation of mirror plane when compared with each other. Overall our results provide a comprehensive analysis on the evolutionary relationship of the three structural nif genes, nifK, nifD and nifH, respectively, in the context of codon usage bias, GC content relationship and amino acid composition of the encoded proteins and exploration of crucial statistical method for the analysis of positive data with non-constant variance to identify the shape factors of codon adaptation index.

Antagonistic Functions of USAG-1 and RUNX2 during Tooth Development.

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Yumiko Togo

Full Text Available Supernumerary teeth and tooth agenesis are common morphological anomalies in humans. We previously obtained evidence that supernumerary maxillary incisors form as a result of the successive development of the rudimentary maxillary incisor tooth germ in Usag-1 null mice. The development of tooth germs is arrested in Runx2 null mice, and such mice also exhibit lingual epithelial buds associated with the upper molars and incisors. The aim of this study is to investigate the potential crosstalk between Usag-1 and Runx2 during tooth development. In the present study, three interesting phenomena were observed in double null Usag-1-/-/Runx2-/- mice: the prevalence of supernumerary teeth was lower than in Usag-1 null mice; tooth development progressed further compared than in Runx2 null mice; and the frequency of molar lingual buds was lower than in Runx2 null mice. Therefore, we suggest that RUNX2 and USAG-1 act in an antagonistic manner. The lingual bud was completely filled with odontogenic epithelial Sox2-positive cells in the Usag-1+/+/Runx2-/- mice, whereas almost no odontogenic epithelial Sox2-positive cells contributed to supernumerary tooth formation in the rudimentary maxillary incisors of the Usag-1-/-/Runx2+/+ mice. Our findings suggest that RUNX2 directly or indirectly prevents the differentiation and/or proliferation of odontogenic epithelial Sox2-positive cells. We hypothesize that RUNX2 inhibits the bone morphogenetic protein (BMP and/or Wnt signaling pathways regulated by USAG-1, whereas RUNX2 expression is induced by BMP signaling independently of USAG-1.

Biased Immunoglobulin Light Chain Gene Usage in the Shark.

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Iacoangeli, Anna; Lui, Anita; Naik, Ushma; Ohta, Yuko; Flajnik, Martin; Hsu, Ellen

2015-10-15

This study of a large family of κ L chain clusters in nurse shark completes the characterization of its classical Ig gene content (two H chain isotypes, μ and ω, and four L chain isotypes, κ, λ, σ, and σ-2). The shark κ clusters are minigenes consisting of a simple VL-JL-CL array, where V to J recombination occurs over an ~500-bp interval, and functional clusters are widely separated by at least 100 kb. Six out of ~39 κ clusters are prerearranged in the germline (germline joined). Unlike the complex gene organization and multistep assembly process of Ig in mammals, each shark Ig rearrangement, somatic or in the germline, appears to be an independent event localized to the minigene. This study examined the expression of functional, nonproductive, and sterile transcripts of the κ clusters compared with the other three L chain isotypes. κ cluster usage was investigated in young sharks, and a skewed pattern of split gene expression was observed, one similar in functional and nonproductive rearrangements. These results show that the individual activation of the spatially distant κ clusters is nonrandom. Although both split and germline-joined κ genes are expressed, the latter are prominent in young animals and wane with age. We speculate that, in the shark, the differential activation of the multiple isotypes can be advantageously used in receptor editing. Copyright © 2015 by The American Association of Immunologists, Inc.

Mutation Pattern of Paired Immunoglobulin Heavy and Light Variable Domains in Chronic Lymphocytic Leukemia B Cells

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Ghiotto, Fabio; Marcatili, Paolo; Tenca, Claudya; Calevo, Maria Grazia; Yan, Xiao-Jie; Albesiano, Emilia; Bagnara, Davide; Colombo, Monica; Cutrona, Giovanna; Chu, Charles C; Morabito, Fortunato; Bruno, Silvia; Ferrarini, Manlio; Tramontano, Anna; Fais, Franco; Chiorazzi, Nicholas

2011-01-01

B-cell chronic lymphocytic leukemia (CLL) patients display leukemic clones bearing either germline or somatically mutated immunoglobulin heavy variable (IGHV ) genes. Most information on CLL immunoglobulins (Igs), such as the definition of stereotyped B-cell receptors (BCRs), was derived from germline unmutated Igs. In particular, detailed studies on the distribution and nature of mutations in paired heavy- and light-chain domains of CLL clones bearing mutated Igs are lacking. To address the somatic hyper-mutation dynamics of CLL Igs, we analyzed the mutation pattern of paired IGHV–diversity-joining (IGHV-D-J ) and immunoglobulin kappa/lambda variable-joining (IGK/LV-J ) rearrangements of 193 leukemic clones that displayed ≥2% mutations in at least one of the two immunoglobulin variable (IGV ) genes (IGHV and/or IGK/LV ). The relationship between the mutation frequency in IGHV and IGK/LV complementarity determining regions (CDRs) and framework regions (FRs) was evaluated by correlation analysis. Replacement (R) mutation frequency within IGK/LV chain CDRs correlated significantly with mutation frequency of paired IGHV CDRs in λ but not κ isotype CLL clones. CDRs of IGKV-J rearrangements displayed a lower percentage of R mutations than IGHVs. The frequency/pattern of mutations in kappa CLL Igs differed also from that in κ-expressing normal B cells described in the literature. Instead, the mutation frequency within the FRs of IGHV and either IGKV or IGLV was correlated. Notably, the amount of diversity introduced by replaced amino acids was comparable between IGHVs and IGKVs. The data indicate a different mutation pattern between κ and λ isotype CLL clones and suggest an antigenic selection that, in κ samples, operates against CDR variation. PMID:21785810

Synonymous Codon Usage Analysis of Thirty Two Mycobacteriophage Genomes

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Sameer Hassan

2009-01-01

Full Text Available Synonymous codon usage of protein coding genes of thirty two completely sequenced mycobacteriophage genomes was studied using multivariate statistical analysis. One of the major factors influencing codon usage is identified to be compositional bias. Codons ending with either C or G are preferred in highly expressed genes among which C ending codons are highly preferred over G ending codons. A strong negative correlation between effective number of codons (Nc and GC3s content was also observed, showing that the codon usage was effected by gene nucleotide composition. Translational selection is also identified to play a role in shaping the codon usage operative at the level of translational accuracy. High level of heterogeneity is seen among and between the genomes. Length of genes is also identified to influence the codon usage in 11 out of 32 phage genomes. Mycobacteriophage Cooper is identified to be the highly biased genome with better translation efficiency comparing well with the host specific tRNA genes.

Comprehensive analysis of the codon usage patterns in the envelope glycoprotein E2 gene of the classical swine fever virus.

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Ye Chen

Full Text Available The classical swine fever virus (CSFV, circulating worldwide, is a highly contagious virus. Since the emergence of CSFV, it has caused great economic loss in swine industry. The envelope glycoprotein E2 gene of the CSFV is an immunoprotective antigen that induces the immune system to produce neutralizing antibodies. Therefore, it is essential to study the codon usage of the E2 gene of the CSFV. In this study, 140 coding sequences of the E2 gene were analyzed. The value of effective number of codons (ENC showed low codon usage bias in the E2 gene. Our study showed that codon usage could be described mainly by mutation pressure ENC plot analysis combined with principal component analysis (PCA and translational selection-correlation analysis between the general average hydropathicity (Gravy and aromaticity (Aroma, and nucleotides at the third position of codons (A3s, T3s, G3s, C3s and GC3s. Furthermore, the neutrality analysis, which explained the relationship between GC12s and GC3s, revealed that natural selection had a key role compared with mutational bias during the evolution of the E2 gene. These results lay a foundation for further research on the molecular evolution of CSFV.

Major prognostic value of complex karyotype in addition to TP53 and IGHV mutational status in first-line chronic lymphocytic leukemia.

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Le Bris, Yannick; Struski, Stéphanie; Guièze, Romain; Rouvellat, Caroline; Prade, Naïs; Troussard, Xavier; Tournilhac, Olivier; Béné, Marie C; Delabesse, Eric; Ysebaert, Loïc

2017-12-01

Chronic lymphocytic leukemia (CLL) is a lymphoproliferative disorder of remarkable heterogeneity as demonstrated by cytogenetics and molecular analyses. Complex karyotype (CK), TP53 deletions and/or mutations (TP53 disruption), IGVH mutational status, and, more recently, recurrent somatic mutations have been identified as prognostic markers in CLL. On a cohort of 110 patients with CLL treated with first-line fludarabin, cyclophosphamide, and rituximab treatment compared with 33 untreated (watch and wait) patients with CLL, we report more frequent complex karyotypes (34 vs 15%; P = .05), unmutated IGHV (70 vs 21%; P < .0001), ATM deletion (25 vs 6%, P = .02), and NOTCH mutation (3 vs 17%, P = .04). Among treated patients, 39 relapsed during the follow-up period. These patients were characterized before treatment by a higher incidence of trisomy 12 (38 vs 11%, P < .001) and TP53 disruption (31 vs 4%, P = .0002). A significantly shorter 5-year overall survival was found for treated patients with CK (72.4 vs 85.8%; P = .007), unmutated IGHV (70 vs 100%; P = .04), or TP53 disruption (55.7 vs 82.7%; P < .0001). Three risk groups were defined based on the status of TP53 disruption or unmutated IGVH, which differed significantly in terms of 5-year overall survival. Moreover, the presence of CK impacted pejoratively 5-year overall survival and progression-free survival in all these 3 groups. Conventional karyotyping therefore appears to be of value, CK being an additional factor, undetectable in classical FISH, in patients with CLL at the stage when therapy becomes required. Copyright © 2016 John Wiley & Sons, Ltd.

Primary cutaneous B-cell lymphoma is associated with somatically hypermutated immunoglobulin variable genes and frequent use of VH1-69 and VH4-59 segments.

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Perez, M; Pacchiarotti, A; Frontani, M; Pescarmona, E; Caprini, E; Lombardo, G A; Russo, G; Faraggiana, T

2010-03-01

Accurate assessment of the somatic mutational status of clonal immunoglobulin variable region (IgV) genes is relevant in elucidating tumour cell origin in B-cell lymphoma; virgin B cells bear unmutated IgV genes, while germinal centre and postfollicular B cells carry mutated IgV genes. Furthermore, biases in the IgV repertoire and distribution pattern of somatic mutations indicate a possible antigen role in the pathogenesis of B-cell malignancies. This work investigates the cellular origin and antigenic selection in primary cutaneous B-cell lymphoma (PCBCL). We analysed the nucleotide sequence of clonal IgV heavy-chain gene (IgVH) rearrangements in 51 cases of PCBCL (25 follicle centre, 19 marginal zone and seven diffuse large B-cell lymphoma, leg-type) and compared IgVH sequences with their closest germline segment in the GenBank database. Molecular data were then correlated with histopathological features. We showed that all but one of the 51 IgVH sequences analysed exhibited extensive somatic hypermutations. The detected mutation rate ranged from 1.6% to 21%, with a median rate of 9.8% and was independent of PCBCL histotype. Calculation of antigen-selection pressure showed that 39% of the mutated IgVH genes displayed a number of replacement mutations and silent mutations in a pattern consistent with antigenic selection. Furthermore, two segments, VH1-69 (12%) and VH4-59 (14%), were preferentially used in our case series. Data indicate that neoplastic B cells of PBCBL have experienced germinal centre reaction and also suggest that the involvement of IgVH genes is not entirely random in PCBCL and that common antigen epitopes could be pathologically relevant in cutaneous lymphomagenesis.

Positive selection for unpreferred codon usage in eukaryotic genomes

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Galagan James E

2007-07-01

Full Text Available Abstract Background Natural selection has traditionally been understood as a force responsible for pushing genes to states of higher translational efficiency, whereas lower translational efficiency has been explained by neutral mutation and genetic drift. We looked for evidence of directional selection resulting in increased unpreferred codon usage (and presumably reduced translational efficiency in three divergent clusters of eukaryotic genomes using a simple optimal-codon-based metric (Kp/Ku. Results Here we show that for some genes natural selection is indeed responsible for causing accelerated unpreferred codon substitution, and document the scope of this selection. In Cryptococcus and to a lesser extent Drosophila, we find many genes showing a statistically significant signal of selection for unpreferred codon usage in one or more lineages. We did not find evidence for this type of selection in Saccharomyces. The signal of positive selection observed from unpreferred synonymous codon substitutions is coincident in Cryptococcus and Drosophila with the distribution of upstream open reading frames (uORFs, another genic feature known to reduce translational efficiency. Functional enrichment analysis of genes exhibiting low Kp/Ku ratios reveals that genes in regulatory roles are particularly subject to this type of selection. Conclusion Through genome-wide scans, we find recent selection for unpreferred codon usage at approximately 1% of genetic loci in a Cryptococcus and several genes in Drosophila. Unpreferred codons can impede translation efficiency, and we find that genes with translation-impeding uORFs are enriched for this selection signal. We find that regulatory genes are particularly likely to be subject to selection for unpreferred codon usage. Given that expression noise can propagate through regulatory cascades, and that low translational efficiency can reduce expression noise, this finding supports the hypothesis that translational

Next generation sequencing reveals skewing of the T and B cell receptor repertoires in patients with Wiskott Aldrich syndrome

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Amy E O'Connell

2014-07-01

Full Text Available The Wiskott Aldrich syndrome (WAS is due to mutations of the WAS gene encoding for the cytoskeletal WAS protein (WASp, leading to abnormal downstream signaling from the T cell and B cell antigen receptors (TCR, BCR. We hypothesized that the impaired signaling through the TCR and BCR in WAS would subsequently lead to aberrations in the immune repertoire of WAS patients. Using next generation sequencing, the T cell receptor beta (TRB and B cell immunoglobulin heavy chain (IGH repertoires of 8 patients with WAS and 6 controls were sequenced. Clonal expansions were identified within memory CD4+ cells, as well as in total, naïve and memory CD8+ cells from WAS patients. In the B cell compartment, WAS patient IGH repertoires were also clonally expanded and showed skewed usage of IGHV and IGHJ genes, and increased usage of IGHG constant genes, compared with controls. To our knowledge, this is the first study that demonstrates significant abnormalities of the immune repertoire in WAS patients using next generation sequencing.

Inheritance of resistance to races 69 and 453 of Colletotrichum lindemuthianum in the common bean

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Juliana P. Poletine

2000-01-01

Full Text Available The cultivars, AB 136 and G 2333 both resistant to Colletotrichum lindemuthianum races 69 and 453, were crossed with the cultivars Michelite and Perry Marrow (susceptible to both races, with Dark Red Kidney and Cornell 49242 (resistant to both races and F1 and F2 generations were obtained. Plants were inoculated using a spore suspension at 1.2 x 10(6 concentration. The reaction of F1 and F2 populations showed that Dark Red Kidney, Cornell 49242 and AB 136 cultivars had the dominant genes A (Co-1, Are (Co-2 and Co-6, respectively, was conferring resistance to races 69 and 453. The segregation data obtained from F2 populations indicated that G 2333 carried two dominant resistance genes Co-5 gene and another one Co-7 for 69 and 453 races. The dominant genes in G 2333 and its resistance to C. lindemuthianum race could be transferred to provide anthracnose resistance to susceptible cultivars relatively easy.Os cultivares AB 136 e G 2333 ambos resistentes às raças 69 e 453 de Colletotrichum lindemuthianum foram cruzados com os cultivares Michelite e Perry Marrow (suscetíveis à ambas as raças e com Dark Red Kidney e Cornell 49242 (resistentes à ambas as raças e, obtidas as gerações F1 e F2. As plantas foram inoculadas com uma suspensão de esporos, utilizando-se uma concentração de 1,2 x 10(6 esporos/ml de água. As reações das populações F1 e F2 evidenciaram que os cultivares Dark Red Kidney; Cornell 49242 e AB 136 possuem, respectivamente, os genes dominantes A (Co-1 Are (Co-2 e Co-6, os quais conferiram a resistência às raças 69 e 453. Os dados de segregação obtidos nas populações F2 indicaram que G 2333 carrega os genes dominantes de resistência Co-5 e Co-7. Os genes dominantes presentes em G 2333 e sua resistência às raças de C. lindemuthianum, poderão serem transferidos para cultivares suscetíveis com relativa facilidade.

Molecular analysis of immunoglobulin variable genes supports a germinal center experienced normal counterpart in primary cutaneous diffuse large B-cell lymphoma, leg-type.

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Pham-Ledard, Anne; Prochazkova-Carlotti, Martina; Deveza, Mélanie; Laforet, Marie-Pierre; Beylot-Barry, Marie; Vergier, Béatrice; Parrens, Marie; Feuillard, Jean; Merlio, Jean-Philippe; Gachard, Nathalie

2017-11-01

Immunophenotype of primary cutaneous diffuse large B-cell lymphoma, leg-type (PCLBCL-LT) suggests a germinal center-experienced B lymphocyte (BCL2+ MUM1+ BCL6+/-). As maturation history of B-cell is "imprinted" during B-cell development on the immunoglobulin gene sequence, we studied the structure and sequence of the variable part of the genes (IGHV, IGLV, IGKV), immunoglobulin surface expression and features of class switching in order to determine the PCLBCL-LT cell of origin. Clonality analysis with BIOMED2 protocol and VH leader primers was done on DNA extracted from frozen skin biopsies on retrospective samples from 14 patients. The clonal DNA IGHV sequence of the tumor was aligned and compared with the closest germline sequence and homology percentage was calculated. Superantigen binding sites were studied. Features of selection pressure were evaluated with the multinomial Lossos model. A functional monoclonal sequence was observed in 14 cases as determined for IGHV (10), IGLV (2) or IGKV (3). IGV mutation rates were high (>5%) in all cases but one (median:15.5%), with superantigen binding sites conservation. Features of selection pressure were identified in 11/12 interpretable cases, more frequently negative (75%) than positive (25%). Intraclonal variation was detected in 3 of 8 tumor specimens with a low rate of mutations. Surface immunoglobulin was an IgM in 12/12 cases. FISH analysis of IGHM locus, deleted during class switching, showed heterozygous IGHM gene deletion in half of cases. The genomic PCR analysis confirmed the deletions within the switch μ region. IGV sequences were highly mutated but functional, with negative features of selection pressure suggesting one or more germinal center passage(s) with somatic hypermutation, but superantigen (SpA) binding sites conservation. Genetic features of class switch were observed, but on the non functional allele and co-existing with primary isotype IgM expression. These data suggest that cell-of origin is

The translocation (6;9) (p23;q34) shows consistent rearrangement of two genes and defines a myeloproliferative disorder with specific clinical features

NARCIS (Netherlands)

Soekarman, D.; von Lindern, M.; Daenen, S.; de Jong, B.; Fonatsch, C.; Heinze, B.; Bartram, C.; Hagemeijer, A.; Grosveld, G.

1992-01-01

Translocation (6;9)(p23;q34) is a cytogenetic aberration that can be found in specific subtypes of both acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). This translocation is associated with an unfavourable prognosis. Recently, the genes involved in the t(6;9) were isolated and

Expression and molecular evolution of two DREB1 genes in black poplar (Populus nigra.

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Yanguang Chu

Full Text Available Environmental stresses such as low temperature, drought, and high salinity significantly affect plant growth and yield. As selective forces, these adverse factors play essential roles in shaping phenotypic variation in plant populations. Black poplar (Populus nigra is an economically and ecologically important forest tree species with widely distributed populations and is thus suitable for experiments detecting evolutionary footprints left by stress. Here, we performed expression and evolutionary analysis of two duplicated DREB A1-subgroup (DREB1 genes, PnDREB68 and PnDREB69, encoding transcription factors that are involved in stress responses. The two genes showed partially overlapping but distinct expression patterns in response to stresses. These genes were strongly and rapidly induced by cold stress in leaves, stems, and roots. In leaf tissue, dehydration stress induced the expression of PnDREB68 but not PnDREB69. PnDREB69 displayed more rapid responses and longer expression durations than PnDREB68 under salt and ABA stress, respectively. Based on single nucleotide polymorphism (SNP analysis, we found significant population genetic differentiation, with a greater FST value (0.09189 for PnDREB69 than for PnDREB68 (0.07743. Nucleotide diversity analysis revealed a two-fold higher πT for PnDREB68 than for PnDREB69 (0.00563 vs. 0.00243, reflecting strong purifying selection acting on the former. The results suggest that positive selection acted on PnDREB69, as evidenced by neutral testing using Tajima's D statistic. The distinct selective forces to which each of the genes was subjected may be associated with expression divergence. Linkage disequilibrium (LD was low for the sequenced region, with a higher level for PnDREB68 than for PnDREB69. Additionally, analysis of the relationship among carbon isotope ratios, SNP classes and gene expression, together with motif and domain analysis, suggested that 14 polymorphisms within the two genes may be

P-value based visualization of codon usage data

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Fricke Wolfgang

2006-06-01

Full Text Available Abstract Two important and not yet solved problems in bacterial genome research are the identification of horizontally transferred genes and the prediction of gene expression levels. Both problems can be addressed by multivariate analysis of codon usage data. In particular dimensionality reduction methods for visualization of multivariate data have shown to be effective tools for codon usage analysis. We here propose a multidimensional scaling approach using a novel similarity measure for codon usage tables. Our probabilistic similarity measure is based on P-values derived from the well-known chi-square test for comparison of two distributions. Experimental results on four microbial genomes indicate that the new method is well-suited for the analysis of horizontal gene transfer and translational selection. As compared with the widely-used correspondence analysis, our method did not suffer from outlier sensitivity and showed a better clustering of putative alien genes in most cases.

Safety and Usage of C1-Inhibitor in Hereditary Angioedema

DEFF Research Database (Denmark)

Riedl, Marc A; Bygum, Anette; Lumry, William

2016-01-01

, international patient registry documented widespread implementation of pnfC1-INH self-administration outside of a health care setting consistent with current HAE guidelines. These real-world data revealed pnfC1-INH usage for a variety of reasons in patients with HAE and showed a high level of safety regardless...... of this study was to describe safety and usage patterns of pnfC1-INH. METHODS: A multicenter, observational, registry was conducted between 2010 and 2014 at 30 United States and 7 European sites to obtain both prospective (occurring after enrollment) and retrospective (occurring before enrollment) safety...... and usage data on subjects receiving pnfC1-INH for any reason. RESULTS: Of 343 enrolled patients, 318 received 1 or more doses of pnfC1-INH for HAE attacks (11,848 infusions) or for prophylaxis (3142 infusions), comprising the safety population. Median dosages per infusion were 10.8 IU/kg (attack treatment...

The Selective Advantage of Synonymous Codon Usage Bias in Salmonella.

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Gerrit Brandis

2016-03-01

Full Text Available The genetic code in mRNA is redundant, with 61 sense codons translated into 20 different amino acids. Individual amino acids are encoded by up to six different codons but within codon families some are used more frequently than others. This phenomenon is referred to as synonymous codon usage bias. The genomes of free-living unicellular organisms such as bacteria have an extreme codon usage bias and the degree of bias differs between genes within the same genome. The strong positive correlation between codon usage bias and gene expression levels in many microorganisms is attributed to selection for translational efficiency. However, this putative selective advantage has never been measured in bacteria and theoretical estimates vary widely. By systematically exchanging optimal codons for synonymous codons in the tuf genes we quantified the selective advantage of biased codon usage in highly expressed genes to be in the range 0.2-4.2 x 10-4 per codon per generation. These data quantify for the first time the potential for selection on synonymous codon choice to drive genome-wide sequence evolution in bacteria, and in particular to optimize the sequences of highly expressed genes. This quantification may have predictive applications in the design of synthetic genes and for heterologous gene expression in biotechnology.

Complement Factor H Y402H and LOC387715 A69S Polymorphisms in Association with Age-Related Macular Degeneration in Iran.

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Nazari Khanamiri, Hossein; Ghasemi Falavarjani, Khalil; Sanati, Mohammad Hossein; Aryan, Hajar; Irani, Alireza; Hashemi, Masih; Modarres, Mehdi; Parvaresh, Mohammad Mehdi; Nikeghbali, Aminollah

2014-04-01

To determine the frequency of complement factor H (Y402H) and age related macular degeneration susceptibility gene 2 (A69S) single nucleotide polymorphisms in patients with age-related macular degeneration (AMD) and in matched non-AMD controls in an Iranian population. Seventy patients with AMD and 86 age- and sex-matched controls were recruited and examined. Peripheral blood sample was obtained from all subjects for DNA extraction and direct sequencing of Y402H and A69S genes. Odds ratios (ORs) with 95% confidence intervals (CIs) for the association of Y402H and A69S polymorphisms with AMD were determined. The frequencies of both homozygous and heterozygous genotypes were significantly higher in cases than controls for both Y402H and A69S polymorphisms. In comparison to the wild genotypes, OR for AMD associated with Y402H and A69S polymorphisms were 1.9 (95% CI, 1.1-3.2) and 2.2 (95%CI, 1.6-3.1), respectively. Joint risk analysis considering both genes revealed a higher risk of AMD when polymorphisms were present for both genes. Y402H and A69S polymorphisms were strongly associated with AMD in this Iranian population.

Complement Factor H Y402H and LOC387715 A69S Polymorphisms in Association with Age-Related Macular Degeneration in Iran

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Hossein Nazari Khanamiri

2014-01-01

Full Text Available Purpose: To determine the frequency of complement factor H (Y402H and age related macular degeneration susceptibility gene 2 (A69S single nucleotide polymorphisms in patients with age-related macular degeneration (AMD and in matched non-AMD controls in an Iranian population. Methods: Seventy patients with AMD and 86 age- and sex-matched controls were recruited and examined. Peripheral blood sample was obtained from all subjects for DNA extraction and direct sequencing of Y402H and A69S genes. Odds ratios (ORs with 95% confidence intervals (CIs for the association of Y402H and A69S polymorphisms with AMD were determined. Results: The frequencies of both homozygous and heterozygous genotypes were significantly higher in cases than controls for both Y402H and A69S polymorphisms. In comparison to the wild genotypes, OR for AMD associated with Y402H and A69S polymorphisms were 1.9 (95% CI, 1.1-3.2 and 2.2 (95%CI, 1.6-3.1, respectively. Joint risk analysis considering both genes revealed a higher risk of AMD when polymorphisms were present for both genes. Conclusion: Y402H and A69S polymorphisms were strongly associated with AMD in this Iranian population.

Diversity of immunoglobulin lambda light chain gene usage over developmental stages in the horse.

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Tallmadge, Rebecca L; Tseng, Chia T; Felippe, M Julia B

2014-10-01

To further studies of neonatal immune responses to pathogens and vaccination, we investigated the dynamics of B lymphocyte development and immunoglobulin (Ig) gene diversity. Previously we demonstrated that equine fetal Ig VDJ sequences exhibit combinatorial and junctional diversity levels comparable to those of adult Ig VDJ sequences. Herein, RACE clones from fetal, neonatal, foal, and adult lymphoid tissue were assessed for Ig lambda light chain combinatorial, junctional, and sequence diversity. Remarkably, more lambda variable genes (IGLV) were used during fetal life than later stages and IGLV gene usage differed significantly with time, in contrast to the Ig heavy chain. Junctional diversity measured by CDR3L length was constant over time. Comparison of Ig lambda transcripts to germline revealed significant increases in nucleotide diversity over time, even during fetal life. These results suggest that the Ig lambda light chain provides an additional dimension of diversity to the equine Ig repertoire. Copyright © 2014 Elsevier Ltd. All rights reserved.

Codon usage vis-a-vis start and stop codon context analysis of three ...

Indian Academy of Sciences (India)

To understand the variation in genomic composition and its effect on codon usage, we performed the comparative analysis of codon usage and nucleotide usage in the genes of three dicots, Glycine max, Arabidopsis thaliana and Medicago truncatula. The dicot genes were found to be A/T rich and have predominantly ...

Analysis of synonymous codon usage patterns in the genus Rhizobium.

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Wang, Xinxin; Wu, Liang; Zhou, Ping; Zhu, Shengfeng; An, Wei; Chen, Yu; Zhao, Lin

2013-11-01

The codon usage patterns of rhizobia have received increasing attention. However, little information is available regarding the conserved features of the codon usage patterns in a typical rhizobial genus. The codon usage patterns of six completely sequenced strains belonging to the genus Rhizobium were analysed as model rhizobia in the present study. The relative neutrality plot showed that selection pressure played a role in codon usage in the genus Rhizobium. Spearman's rank correlation analysis combined with correspondence analysis (COA) showed that the codon adaptation index and the effective number of codons (ENC) had strong correlation with the first axis of the COA, which indicated the important role of gene expression level and the ENC in the codon usage patterns in this genus. The relative synonymous codon usage of Cys codons had the strongest correlation with the second axis of the COA. Accordingly, the usage of Cys codons was another important factor that shaped the codon usage patterns in Rhizobium genomes and was a conserved feature of the genus. Moreover, the comparison of codon usage between highly and lowly expressed genes showed that 20 unique preferred codons were shared among Rhizobium genomes, revealing another conserved feature of the genus. This is the first report of the codon usage patterns in the genus Rhizobium.

Genome-wide analysis of codon usage bias in Ebolavirus.

Science.gov (United States)

Cristina, Juan; Moreno, Pilar; Moratorio, Gonzalo; Musto, Héctor

2015-01-22

Ebola virus (EBOV) is a member of the family Filoviridae and its genome consists of a 19-kb, single-stranded, negative sense RNA. EBOV is subdivided into five distinct species with different pathogenicities, being Zaire ebolavirus (ZEBOV) the most lethal species. The interplay of codon usage among viruses and their hosts is expected to affect overall viral survival, fitness, evasion from host's immune system and evolution. In the present study, we performed comprehensive analyses of codon usage and composition of ZEBOV. Effective number of codons (ENC) indicates that the overall codon usage among ZEBOV strains is slightly biased. Different codon preferences in ZEBOV genes in relation to codon usage of human genes were found. Highly preferred codons are all A-ending triplets, which strongly suggests that mutational bias is a main force shaping codon usage in ZEBOV. Dinucleotide composition also plays a role in the overall pattern of ZEBOV codon usage. ZEBOV does not seem to use the most abundant tRNAs present in the human cells for most of their preferred codons. Copyright © 2014 Elsevier B.V. All rights reserved.

Determination of HIV-1 co-receptor usage.

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Cavarelli, Mariangela; Scarlatti, Gabriella

2014-01-01

Human immunodeficiency virus type I (HIV-1) infects target cells through interaction with the CD4 molecule and chemokine receptors, mainly the β-chemokine receptor 5 (CCR5) and the α-chemokine receptor 4 (CXCR4). Viral isolates can be phenotypically classified based on the co-receptor they utilize to infect target cells. In this chapter, methods to determine the co-receptor usage of HIV-1 variants are described.

Analysis of amino acid and codon usage in Paramecium bursaria.

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Dohra, Hideo; Fujishima, Masahiro; Suzuki, Haruo

2015-10-07

The ciliate Paramecium bursaria harbors the green-alga Chlorella symbionts. We reassembled the P. bursaria transcriptome to minimize falsely fused transcripts, and investigated amino acid and codon usage using the transcriptome data. Surface proteins preferentially use smaller amino acid residues like cysteine. Unusual synonymous codon and amino acid usage in highly expressed genes can reflect a balance between translational selection and other factors. A correlation of gene expression level with synonymous codon or amino acid usage is emphasized in genes down-regulated in symbiont-bearing cells compared to symbiont-free cells. Our results imply that the selection is associated with P. bursaria-Chlorella symbiosis. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Complexity and dynamics of HIV-1 chemokine receptor usage in a multidrug-resistant adolescent.

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Cavarelli, Mariangela; Mainetti, Lara; Pignataro, Angela Rosa; Bigoloni, Alba; Tolazzi, Monica; Galli, Andrea; Nozza, Silvia; Castagna, Antonella; Sampaolo, Michela; Boeri, Enzo; Scarlatti, Gabriella

2014-12-01

Maraviroc (MVC) is licensed in clinical practice for patients with R5 virus and virological failure; however, in anecdotal reports, dual/mixed viruses were also inhibited. We retrospectively evaluated the evolution of HIV-1 coreceptor tropism in plasma and peripheral blood mononuclear cells (PBMCs) of an infected adolescent with a CCR5/CXCR4 Trofile profile who experienced an important but temporary immunological and virological response during a 16-month period of MVC-based therapy. Coreceptor usage of biological viral clones isolated from PBMCs was investigated in U87.CD4 cells expressing wild-type or chimeric CCR5 and CXCR4. Plasma and PBMC-derived viral clones were sequenced to predict coreceptor tropism using the geno2pheno algorithm from the V3 envelope sequence and pol gene-resistant mutations. From start to 8.5 months of MVC treatment only R5X4 viral clones were observed, whereas at 16 months the phenotype enlarged to also include R5 and X4 clones. Chimeric receptor usage suggested the preferential usage of the CXCR4 coreceptor by the R5X4 biological clones. According to phenotypic data, R5 viruses were susceptible, whereas R5X4 and X4 viruses were resistant to RANTES and MVC in vitro. Clones at 16 months, but not at baseline, showed an amino acidic resistance pattern in protease and reverse transcription genes, which, however, did not drive their tropisms. The geno2pheno algorithm predicted at baseline R5 viruses in plasma, and from 5.5 months throughout follow-up only CXCR4-using viruses. An extended methodological approach is needed to unravel the complexity of the phenotype and variation of viruses resident in the different compartments of an infected individual. The accurate evaluation of the proportion of residual R5 viruses may guide therapeutic intervention in highly experienced patients with limited therapeutic options.

B lymphocyte selection and age-related changes in VH gene usage in mutant Alicia rabbits.

Science.gov (United States)

Zhu, X; Boonthum, A; Zhai, S K; Knight, K L

1999-09-15

Young Alicia rabbits use VHa-negative genes, VHx and VHy, in most VDJ genes, and their serum Ig is VHa negative. However, as Alicia rabbits age, VHa2 allotype Ig is produced at high levels. We investigated which VH gene segments are used in the VDJ genes of a2 Ig-secreting hybridomas and of a2 Ig+ B cells from adult Alicia rabbits. We found that 21 of the 25 VDJ genes used the a2-encoding genes, VH4 or VH7; the other four VDJ genes used four unknown VH gene segments. Because VH4 and VH7 are rarely found in VDJ genes of normal or young Alicia rabbits, we investigated the timing of rearrangement of these genes in Alicia rabbits. During fetal development, VH4 was used in 60-80% of nonproductively rearranged VDJ genes, and VHx and VHy together were used in 10-26%. These data indicate that during B lymphopoiesis VH4 is preferentially rearranged. However, the percentage of productive VHx- and VHy-utilizing VDJ genes increased from 38% at day 21 of gestation to 89% at birth (gestation day 31), whereas the percentage of VH4-utilizing VDJ genes remained at 15%. These data suggest that during fetal development, either VH4-utilizing B-lineage cells are selectively eliminated, or B cells with VHx- and VHy-utilizing VDJ genes are selectively expanded, or both. The accumulation of peripheral VH4-utilizing a2 B cells with age indicates that these B cells might be selectively expanded in the periphery. We discuss the possible selection mechanisms that regulate VH gene segment usage in rabbit B cells during lymphopoiesis and in the periphery.

Molecular analysis of immunoglobulin genes reveals frequent clonal relatedness in double monoclonal gammopathies.

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Tschumper, R C; Dispenzieri, A; Abraham, R S; Henderson, K J; Jelinek, D F

2013-04-19

Monoclonal gammopathies (MGs) are hematological diseases characterized by high levels of a monoclonal immunoglobulin (Ig) or M-protein. Within this group are patients with more than one M-protein, referred to as double MGs (DMGs). The M-proteins in DMG patients may have different heavy chain (HC) isotypes that are associated with different light chains (LCs), or different HCs that are LC matched. In this study, we examined the clonal relatedness of the M-proteins in the latter type in a cohort of 14 DMG patients. By using PCR, we identified 7/14 DMG patients that expressed two Ig HC isotypes with identical Ig HC variable (IGHV), diversity (IGHD), joining (IGHJ), and complementarity determining region (HCDR3) sequences. Two additional DMG patients had two Ig transcripts using the same IGHV, IGHD and IGHJ genes but with slight differences in variable region or HCDR3 mutations. LC analysis confirmed that a single LC was expressed in 3/7 DMG patients with identical HC transcripts and in the two DMGs with highly similar transcripts. The PCR findings were confirmed by immunofluorescence for HC and LC expression. Clonally related HC-dissimilar/LC-matched DMGs may occur often and defines a new subtype of MG that may serve as a tool for studies of disease pathogenesis.

Molecular analysis of immunoglobulin genes reveals frequent clonal relatedness in double monoclonal gammopathies

International Nuclear Information System (INIS)

Tschumper, R C; Dispenzieri, A; Abraham, R S; Henderson, K J; Jelinek, D F

2013-01-01

Monoclonal gammopathies (MGs) are hematological diseases characterized by high levels of a monoclonal immunoglobulin (Ig) or M-protein. Within this group are patients with more than one M-protein, referred to as double MGs (DMGs). The M-proteins in DMG patients may have different heavy chain (HC) isotypes that are associated with different light chains (LCs), or different HCs that are LC matched. In this study, we examined the clonal relatedness of the M-proteins in the latter type in a cohort of 14 DMG patients. By using PCR, we identified 7/14 DMG patients that expressed two Ig HC isotypes with identical Ig HC variable (IGHV), diversity (IGHD), joining (IGHJ), and complementarity determining region (HCDR3) sequences. Two additional DMG patients had two Ig transcripts using the same IGHV, IGHD and IGHJ genes but with slight differences in variable region or HCDR3 mutations. LC analysis confirmed that a single LC was expressed in 3/7 DMG patients with identical HC transcripts and in the two DMGs with highly similar transcripts. The PCR findings were confirmed by immunofluorescence for HC and LC expression. Clonally related HC-dissimilar/LC-matched DMGs may occur often and defines a new subtype of MG that may serve as a tool for studies of disease pathogenesis

Investigation of associations between NR1D1, RORA and RORB genes and bipolar disorder.

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Yin-Chieh Lai

Full Text Available Several genes that are involved in the regulation of circadian rhythms are implicated in the susceptibility to bipolar disorder (BD. The current study aimed to investigate the relationships between genetic variants in NR1D1 RORA, and RORB genes and BD in the Han Chinese population. We conducted a case-control genetic association study with two samples of BD patients and healthy controls. Sample I consisted of 280 BD patients and 200 controls. Sample II consisted of 448 BD patients and 1770 healthy controls. 27 single nucleotide polymorphisms in the NR1D1, RORA, and RORB genes were genotyped using GoldenGate VeraCode assays in sample I, and 492 markers in the three genes were genotyped using Affymetrix Genome-Wide CHB Array in sample II. Single marker and gene-based association analyses were performed using PLINK. A combined p-value for the joining effects of all markers within a gene was calculated using the rank truncated product method. Multifactor dimensionality reduction (MDR method was also applied to test gene-gene interactions in sample I. All markers were in Hardy-Weinberg equilibrium (P>0.001. In sample I, the associations with BD were observed for rs4774388 in RORA (OR = 1.53, empirical p-value, P = 0.024, and rs1327836 in RORB (OR = 1.75, P = 0.003. In Sample II, there were 45 SNPs showed associations with BD, and the most significant marker in RORA was rs11639084 (OR = 0.69, P = 0.002, and in RORB was rs17611535 (OR = 3.15, P = 0.027. A combined p-value of 1.6×10-6, 0.7, and 1.0 was obtained for RORA, RORB and NR1D1, respectively, indicting a strong association for RORA with the risk of developing BD. A four way interaction was found among markers in NR1D1, RORA, and RORB with the testing accuracy 53.25% and a cross-validation consistency of 8 out of 10. In sample II, 45 markers had empirical p-values less than 0.05. The most significant markers in RORA and RORB genes were rs11639084 (OR = 0.69, P = 0.002, and rs17611535 (OR = 3

MRI usage in a pediatric emergency department: an analysis of usage and usage trends over 5 years

Energy Technology Data Exchange (ETDEWEB)

Scheinfeld, Meir H. [Montefiore Medical Center, Albert Einstein College of Medicine, Department of Radiology, Division of Emergency Radiology, Bronx, NY (United States); Moon, Jee-Young; Wang, Dan [Albert Einstein College of Medicine, Department of Epidemiology and Population Health, Bronx, NY (United States); Fagan, Michele J. [Montefiore Medical Center, Albert Einstein College of Medicine, Department of Pediatrics, Division of Emergency Medicine, Bronx, NY (United States); Davoudzadeh, Reubin [Montefiore Medical Center, Department of Radiology, Bronx, NY (United States); Taragin, Benjamin H. [Montefiore Medical Center, Albert Einstein College of Medicine, Department of Radiology, Division of Pediatric Radiology, Bronx, NY (United States)

2017-03-15

Magnetic resonance imaging (MRI) usage has anecdotally increased due to the principles of ALARA and the desire to Image Gently. Aside from a single abstract in the emergency medicine literature, pediatric emergency department MRI usage has not been described. Our objective was to determine whether MRI use is indeed increasing at a high-volume urban pediatric emergency department with 24/7 MRI availability. Also, we sought to determine which exams, time periods and demographics influenced the trend. Institutional Review Board exemption was obtained. Emergency department patient visit and exam data were obtained from the hospital database for the 2011-2015 time period. MRI usage data were normalized using emergency department patient visit data to determine usage rates. The z-test was used to compare MRI use by gender. The chi-square test was used to test for trends in MRI usage during the study period and in patient age. MRI usage for each hour and each weekday were tabulated to determine peak and trough usage times. MRI usage rate per emergency department patient visit was 0.36%. Headache, pain and rule-out appendicitis were the most common indications for neuroradiology, musculoskeletal and trunk exams, respectively. Usage in female patients was significantly greater than in males (0.42% vs. 0.29%, respectively, P<0.001). Usage significantly increased during the 5-year period (P<0.001). Use significantly increased from age 3 to 17 (0.011% to 1.1%, respectively, P<0.001). Sixty percent of exams were performed after-hours, the highest volume during the 10 p.m. hour and lowest between 4 a.m. and 9 a.m. MRI use was highest on Thursdays and lowest on Sundays (MRI on 0.45% and 0.22% of patients, respectively). MRI use in children increased during the study period, most notably in females, on weekdays and after-hours. (orig.)

Analysis of codon usage patterns in Morus notabilis based on genome and transcriptome data.

Science.gov (United States)

Wen, Yan; Zou, Ziliang; Li, Hongshun; Xiang, Zhonghuai; He, Ningjia

2017-06-01

Codons play important roles in regulating gene expression levels and mRNA half-lives. However, codon usage and related studies in multicellular organisms still lag far behind those in unicellular organisms. In this study, we describe for the first time genome-wide patterns of codon bias in Morus notabilis (mulberry tree), and analyze genome-wide codon usage in 12 other species within the order Rosales. The codon usage of M. notabilis was affected by nucleotide composition, mutation pressure, nature selection, and gene expression level. Translational selection optimal codons were identified and highly expressed genes of M. notabilis tended to use the optimal codons. Genes with higher expression levels have shorter coding region and lower amino acid complexity. Housekeeping genes showed stronger translational selection, which, notably, was not caused by the large differences between the expression level of housekeeping genes and other genes.

Combination of the Endogenous lhcsr1 Promoter and Codon Usage Optimization Boosts Protein Expression in the Moss Physcomitrella patens

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Manuel Hiss

2017-10-01

Full Text Available The moss Physcomitrella patens is used both as an evo-devo model and biotechnological production system for metabolites and pharmaceuticals. Strong in vivo expression of genes of interest is important for production of recombinant proteins, e.g., selectable markers, fluorescent proteins, or enzymes. In this regard, the choice of the promoter sequence as well as codon usage optimization are two important inside factors to consider in order to obtain optimum protein accumulation level. To reliably quantify fluorescence, we transfected protoplasts with promoter:GFP fusion constructs and measured fluorescence intensity of living protoplasts in a plate reader system. We used the red fluorescent protein mCherry under 2x 35S promoter control as second reporter to normalize for different transfection efficiencies. We derived a novel endogenous promoter and compared deletion variants with exogenous promoters. We used different codon-adapted green fluorescent protein (GFP genes to evaluate the influence of promoter choice and codon optimization on protein accumulation in P. patens, and show that the promoter of the gene of P. patens chlorophyll a/b binding protein lhcsr1 drives expression of GFP in protoplasts significantly (more than twofold better than the commonly used 2x 35S promoter or the rice actin1 promoter. We identified a shortened 677 bp version of the lhcsr1 promoter that retains full activity in protoplasts. The codon optimized GFP yields significantly (more than twofold stronger fluorescence signals and thus demonstrates that adjusting codon usage in P. patens can increase expression strength. In combination, new promotor and codon optimized GFP conveyed sixfold increased fluorescence signal.

Selective forces and mutational biases drive stop codon usage in the human genome: a comparison with sense codon usage.

Science.gov (United States)

Trotta, Edoardo

2016-05-17

The three stop codons UAA, UAG, and UGA signal the termination of mRNA translation. As a result of a mechanism that is not adequately understood, they are normally used with unequal frequencies. In this work, we showed that selective forces and mutational biases drive stop codon usage in the human genome. We found that, in respect to sense codons, stop codon usage was affected by stronger selective forces but was less influenced by neutral mutational biases. UGA is the most frequent termination codon in human genome. However, UAA was the preferred stop codon in genes with high breadth of expression, high level of expression, AT-rich coding sequences, housekeeping functions, and in gene ontology categories with the largest deviation from expected stop codon usage. Selective forces associated with the breadth and the level of expression favoured AT-rich sequences in the mRNA region including the stop site and its proximal 3'-UTR, but acted with scarce effects on sense codons, generating two regions, upstream and downstream of the stop codon, with strongly different base composition. By favouring low levels of GC-content, selection promoted labile local secondary structures at the stop site and its proximal 3'-UTR. The compositional and structural context favoured by selection was surprisingly emphasized in the class of ribosomal proteins and was consistent with sequence elements that increase the efficiency of translational termination. Stop codons were also heterogeneously distributed among chromosomes by a mechanism that was strongly correlated with the GC-content of coding sequences. In human genome, the nucleotide composition and the thermodynamic stability of stop codon site and its proximal 3'-UTR are correlated with the GC-content of coding sequences and with the breadth and the level of gene expression. In highly expressed genes stop codon usage is compositionally and structurally consistent with highly efficient translation termination signals.

Analysis of transcriptome data reveals multifactor constraint on codon usage in Taenia multiceps.

Science.gov (United States)

Huang, Xing; Xu, Jing; Chen, Lin; Wang, Yu; Gu, Xiaobin; Peng, Xuerong; Yang, Guangyou

2017-04-20

Codon usage bias (CUB) is an important evolutionary feature in genomes that has been widely observed in many organisms. However, the synonymous codon usage pattern in the genome of T. multiceps remains to be clarified. In this study, we analyzed the codon usage of T. multiceps based on the transcriptome data to reveal the constraint factors and to gain an improved understanding of the mechanisms that shape synonymous CUB. Analysis of a total of 8,620 annotated mRNA sequences from T. multiceps indicated only a weak codon bias, with mean GC and GC3 content values of 49.29% and 51.43%, respectively. Our analysis indicated that nucleotide composition, mutational pressure, natural selection, gene expression level, amino acids with grand average of hydropathicity (GRAVY) and aromaticity (Aromo) and the effective selection of amino-acids all contributed to the codon usage in T. multiceps. Among these factors, natural selection was implicated as the major factor affecting the codon usage variation in T. multiceps. The codon usage of ribosome genes was affected mainly by mutations, while the essential genes were affected mainly by selection. In addition, 21codons were identified as "optimal codons". Overall, the optimal codons were GC-rich (GC:AU, 41:22), and ended with G or C (except CGU). Furthermore, different degrees of variation in codon usage were found between T. multiceps and Escherichia coli, yeast, Homo sapiens. However, little difference was found between T. multiceps and Taenia pisiformis. In this study, the codon usage pattern of T. multiceps was analyzed systematically and factors affected CUB were also identified. This is the first study of codon biology in T. multiceps. Understanding the codon usage pattern in T. multiceps can be helpful for the discovery of new genes, molecular genetic engineering and evolutionary studies.

Genomic composition factors affect codon usage in porcine genome

African Journals Online (AJOL)

j.khobondo

2015-01-28

Jan 28, 2015 ... The mutational bias hypothesis predicted that genes in the GC-rich regions of the genome ... observed codon divided by its expected frequency at equilibrium. An RSCU value close to 1 indicates lack of bias, ..... study our results points to preferred usage of both C or G and A or T at the synonyms sites as ...

[Comparison of protective properties of the smallpox DNA-vaccine based on the variola virus A30L gene and its variant with modified codon usage].

Science.gov (United States)

Maksiutov, R A; Shchelkunov, S N

2011-01-01

Efficacy of candidate DNA-vaccines based on the variola virus natural gene A30L and artificial gene A30Lopt with modified codon usage, optimized for expression in mammalian cells, was tested. The groups of mice were intracutaneously immunized three times with three-week intervals with candidate DNA-vaccines: pcDNA_A30L or pcDNA_A30Lopt, and in three weeks after the last immunization all mice in the groups were intraperitoneally infected by the ectromelia virus K1 strain in 10 LD50 dose for the estimation of protection. It was shown that the DNA-vaccines based on natural gene A30L and codon-optimized gene A30Lopt elicited virus, thereby neutralizing the antibody response and protected mice from lethal intraperitoneal challenge with the ectromelia virus with lack of statistically significant difference.

Exclusion of homozygous PLCE1 (NPHS3) mutations in 69 families with idiopathic and hereditary FSGS.

LENUS (Irish Health Repository)

Gbadegesin, Rasheed

2009-02-01

Focal and segmental glomerulosclerosis (FSGS) is the most common glomerular cause of end-stage kidney disease (ESKD). Although the etiology of FSGS has not been fully elucidated, recent results from the positional cloning of genes mutated in nephrotic syndromes are now beginning to provide insight into the pathogenesis of these diseases. Mutations in PLCE1\\/NPHS3 have recently been reported as a cause of nephrotic syndrome characterized by diffuse mesangial sclerosis (DMS) histology. One single family with a missense mutation had late onset of the disease that was characterized by FSGS. To further define the role of PLCE1 mutations in the etiology of FSGS, we performed mutational analysis in 69 families with FSGS. A total of 69 families with 231 affected individuals were examined. The median age of disease onset was 26 years (range 1-66 years). Onset of ESKD was at a median age of 35.5 years. Seven variants leading to non-synonymous changes were found, of which only two are new variants (exon 4 c.1682 G>A R561Q, exon 31 c.6518A>G K2173R). No known disease-causing mutations were identified in the families screened. PLCE1\\/NPHS3 mutations are not a cause of FSGS in this cohort. The absence of mutations in PLCE1\\/NPHS3 in this study indicates that there are additional genetic causes of FSGS and that hereditary FSGS is a heterogeneous disease. Kindreds appropriate for genome-wide screening are currently being subjected to analysis with the aim of identifying other genetic causes of FSGS.

Gene-gene combination effect and interactions among ABCA1, APOA1, SR-B1, and CETP polymorphisms for serum high-density lipoprotein-cholesterol in the Japanese population.

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Akihiko Nakamura

Full Text Available BACKGROUND/OBJECTIVE: Gene-gene interactions in the reverse cholesterol transport system for high-density lipoprotein-cholesterol (HDL-C are poorly understood. The present study observed gene-gene combination effect and interactions between single nucleotide polymorphisms (SNPs in ABCA1, APOA1, SR-B1, and CETP in serum HDL-C from a cross-sectional study in the Japanese population. METHODS: The study population comprised 1,535 men and 1,515 women aged 35-69 years who were enrolled in the Japan Multi-Institutional Collaborative Cohort (J-MICC Study. We selected 13 SNPs in the ABCA1, APOA1, CETP, and SR-B1 genes in the reverse cholesterol transport system. The effects of genetic and environmental factors were assessed using general linear and logistic regression models after adjusting for age, sex, and region. PRINCIPAL FINDINGS: Alcohol consumption and daily activity were positively associated with HDL-C levels, whereas smoking had a negative relationship. The T allele of CETP, rs3764261, was correlated with higher HDL-C levels and had the highest coefficient (2.93 mg/dL/allele among the 13 SNPs, which was statistically significant after applying the Bonferroni correction (p<0.001. Gene-gene combination analysis revealed that CETP rs3764261 was associated with high HDL-C levels with any combination of SNPs from ABCA1, APOA1, and SR-B1, although no gene-gene interaction was apparent. An increasing trend for serum HDL-C was also observed with an increasing number of alleles (p<0.001. CONCLUSIONS: The present study identified a multiplier effect from a polymorphism in CETP with ABCA1, APOA1, and SR-B1, as well as a dose-dependence according to the number of alleles present.

Alterations in LMTK2, MSMB and HNF1B gene expression are associated with the development of prostate cancer

International Nuclear Information System (INIS)

Harries, Lorna W; Perry, John RB; McCullagh, Paul; Crundwell, Malcolm

2010-01-01

Genome wide association studies (GWAS) have identified several genetic variants that are associated with prostate cancer. Most of these variants, like other GWAS association signals, are located in non-coding regions of potential candidate genes, and thus could act at the level of the mRNA transcript. We measured the expression and isoform usage of seven prostate cancer candidate genes in benign and malignant prostate by real-time PCR, and correlated these factors with cancer status and genotype at the GWAS risk variants. We determined that levels of LMTK2 transcripts in prostate adenocarcinomas were only 32% of those in benign tissues (p = 3.2 × 10 -7 ), and that an independent effect of genotype at variant rs6465657 on LMTK2 expression in benign (n = 39) and malignant tissues (n = 21) was also evident (P = 0.002). We also identified that whilst HNF1B(C) and MSMB2 comprised the predominant isoforms in benign tissues (90% and 98% of total HNF1B or MSMB expression), HNF1B(B) and MSMB1 were predominant in malignant tissue (95% and 96% of total HNF1B or MSMB expression; P = 1.7 × 10 -7 and 4 × 10 -4 respectively), indicating major shifts in isoform usage. Our results indicate that the amount or nature of mRNA transcripts expressed from the LMTK2, HNF1B and MSMB candidate genes is altered in prostate cancer, and provides further evidence for a role for these genes in this disorder. The alterations in isoform usage we detect highlights the potential importance of alternative mRNA processing and moderation of mRNA stability as potentially important disease mechanisms

7 CFR 6.9 - Information.

Science.gov (United States)

2010-01-01

... 7 Agriculture 1 2010-01-01 2010-01-01 false Information. 6.9 Section 6.9 Agriculture Office of the Secretary of Agriculture IMPORT QUOTAS AND FEES General Provisions § 6.9 Information. Persons desiring information from the Department of Agriculture regarding section 22 or section 8(a), or any action with...

Translational selection on codon usage in the genus Aspergillus.

Science.gov (United States)

Iriarte, Andrés; Sanguinetti, Manuel; Fernández-Calero, Tamara; Naya, Hugo; Ramón, Ana; Musto, Héctor

2012-09-10

Aspergillus is a genus of mold fungi that includes more than 200 described species. Many members of the group are relevant pathogens and other species are economically important. Only one species has been analyzed for codon usage, and this was performed with a small number of genes. In this paper, we report the codon usage patterns of eight completely sequenced genomes which belong to this genus. The results suggest that selection for translational efficiency and accuracy are the major factors shaping codon usage in all of the species studied so far, and therefore they were active in the last common ancestor of the group. Composition and molecular distances analyses show that highly expressed genes evolve slower at synonymous sites. We identified a conserved core of translationally optimal codons and study the tRNA gene pool in each genome. We found that the great majority of preferred triplets match the respective cognate tRNA with more copies in the respective genome. We discuss the possible scenarios that can explain the observed differences among the species analyzed. Finally we highlight the biotechnological application of this research regarding heterologous protein expression. Copyright © 2012 Elsevier B.V. All rights reserved.

Universality and Shannon entropy of codon usage

CERN Document Server

Frappat, L; Sciarrino, A; Sorba, Paul

2003-01-01

The distribution functions of the codon usage probabilities, computed over all the available GenBank data, for 40 eukaryotic biological species and 5 chloroplasts, do not follow a Zipf law, but are best fitted by the sum of a constant, an exponential and a linear function in the rank of usage. For mitochondriae the analysis is not conclusive. A quantum-mechanics-inspired model is proposed to describe the observed behaviour. These functions are characterized by parameters that strongly depend on the total GC content of the coding regions of biological species. It is predicted that the codon usage is the same in all exonic genes with the same GC content. The Shannon entropy for codons, also strongly depending on the exonic GC content, is computed.

In-Depth Analysis of Human Neonatal and Adult IgM Antibody Repertoires

Directory of Open Access Journals (Sweden)

Binbin Hong

2018-02-01

Full Text Available Although high-throughput sequencing and associated bioinformatics technologies have enabled the in-depth, sequence-based characterization of human immune repertoires, only a few studies on a relatively small number of sequences explored the characteristics of antibody repertoires in neonates, with contradictory conclusions. To gain a more comprehensive understanding of the human IgM antibody repertoire, we performed Illumina sequencing and IMGT/HighV-QUEST analysis of IgM heavy chain repertoire of the B lymphocytes from the cord blood (CB of neonates, as well as the repertoire from peripheral blood of healthy human adults (HH. The comparative study revealed unexpectedly high levels of similarity between the neonatal and adult repertoires. In both repertoires, the VDJ gene usage showed no significant difference, and the most frequently used VDJ gene was IGHV4-59, IGHD3-10, and IGHJ3. The average amino acid (aa length of CDR1 (CB: 8.5, HH: 8.4 and CDR2 (CB: 7.6, HH: 7.5, as well as the aa composition and the average hydrophobicity of the CDR3 demonstrated no significant difference between the two repertories. However, the average aa length of CDR3 was longer in the HH repertoire than the CB repertoire (CB: 14.5, HH: 15.5. Besides, the frequencies of aa mutations in CDR1 (CB: 19.33%, HH: 25.84% and CDR2 (CB: 9.26%, HH: 17.82% were higher in the HH repertoire compared to the CB repertoire. Interestingly, the most prominent difference between the two repertoires was the occurrence of N2 addition (CB: 64.87%, HH: 85.69%, a process that occurs during V-D-J recombination for introducing random nucleotide additions between D- and J-gene segments. The antibody repertoire of healthy adults was more diverse than that of neonates largely due to the higher occurrence of N2 addition. These findings may lead to a better understanding of antibody development and evolution pathways and may have potential practical value for facilitating the generation of more

Alterations in LMTK2, MSMB and HNF1B gene expression are associated with the development of prostate cancer

Directory of Open Access Journals (Sweden)

McCullagh Paul

2010-06-01

Full Text Available Abstract Background Genome wide association studies (GWAS have identified several genetic variants that are associated with prostate cancer. Most of these variants, like other GWAS association signals, are located in non-coding regions of potential candidate genes, and thus could act at the level of the mRNA transcript. Methods We measured the expression and isoform usage of seven prostate cancer candidate genes in benign and malignant prostate by real-time PCR, and correlated these factors with cancer status and genotype at the GWAS risk variants. Results We determined that levels of LMTK2 transcripts in prostate adenocarcinomas were only 32% of those in benign tissues (p = 3.2 × 10-7, and that an independent effect of genotype at variant rs6465657 on LMTK2 expression in benign (n = 39 and malignant tissues (n = 21 was also evident (P = 0.002. We also identified that whilst HNF1B(C and MSMB2 comprised the predominant isoforms in benign tissues (90% and 98% of total HNF1B or MSMB expression, HNF1B(B and MSMB1 were predominant in malignant tissue (95% and 96% of total HNF1B or MSMB expression; P = 1.7 × 10-7 and 4 × 10-4 respectively, indicating major shifts in isoform usage. Conclusions Our results indicate that the amount or nature of mRNA transcripts expressed from the LMTK2, HNF1B and MSMB candidate genes is altered in prostate cancer, and provides further evidence for a role for these genes in this disorder. The alterations in isoform usage we detect highlights the potential importance of alternative mRNA processing and moderation of mRNA stability as potentially important disease mechanisms.

HIV type 1 chemokine receptor usage in mother-to-child transmission.

Science.gov (United States)

Salvatori, F; Scarlatti, G

2001-07-01

To investigate the role of the HIV-1 phenotype in mother-to-child HIV-1 transmission, we evaluated coreceptor usage and replication kinetics in chemokine receptor-expressing U87MG.CD4 cells of primary isolates from 32 HIV-1-infected mothers of Italian origin, none under preventive antiretroviral therapy, and from their infected infants. Five of 15 mothers of infected children and 2 of 17 mothers of uninfected children harbored viruses able to use CXCR4 as coreceptor. However, all isolates used CCR5, alone or in association with CXCR4. The replicative capacity in coreceptor-expressing cells of the viral isolates did not differ between the two groups of mothers. All mothers with an R5 virus transmitted a virus with the same coreceptor usage, whereas those four with a multitropic virus transmitted such a virus in one case. Although the presence of a mixed viral population was documented in the mothers, we did not observe transmission solely of X4 viruses. Interestingly, the only child infected with a multitropic virus carried a defective CCR5 allele. Analysis of the env V3 region of the provirus from this child revealed infection with multiple viral variants with a predominance of R5-type over X4-type sequences. These findings show that CCR5 usage of a viral isolate is not a discriminating risk factor for vertical transmission. Furthermore, X4 viruses can be transmitted to the newborn, although less frequently. In particular, we document the transmission of multiple viral variants with different coreceptor usage in a Delta32 CCR5 heterozygous child, and demonstrate that the heterozygous genotype per se does not contribute to the restriction of R5-type virus spread.

dlx and sp6-9 Control optic cup regeneration in a prototypic eye.

Directory of Open Access Journals (Sweden)

Sylvain W Lapan

2011-08-01

Full Text Available Optic cups are a structural feature of diverse eyes, from simple pit eyes to camera eyes of vertebrates and cephalopods. We used the planarian prototypic eye as a model to study the genetic control of optic cup formation and regeneration. We identified two genes encoding transcription factors, sp6-9 and dlx, that were expressed in the eye specifically in the optic cup and not the photoreceptor neurons. RNAi of these genes prevented formation of visible optic cups during regeneration. Planarian regeneration requires an adult proliferative cell population with stem cell-like properties called the neoblasts. We found that optic cup formation occurred only after migration of progressively differentiating progenitor cells from the neoblast population. The eye regeneration defect caused by dlx and sp6-9 RNAi can be explained by a failure to generate these early optic cup progenitors. Dlx and Sp6-9 genes function as a module during the development of diverse animal appendages, including vertebrate and insect limbs. Our work reveals a novel function for this gene pair in the development of a fundamental eye component, and it utilizes these genes to demonstrate a mechanism for total organ regeneration in which extensive cell movement separates new cell specification from organ morphogenesis.

49 CFR 22.69 - Claim process.

Science.gov (United States)

2010-10-01

... 49 Transportation 1 2010-10-01 2010-10-01 false Claim process. 22.69 Section 22.69 Transportation Office of the Secretary of Transportation SHORT-TERM LENDING PROGRAM (STLP) Loan Administration § 22.69 Claim process. After reasonable efforts have been exhausted to collect on a delinquent debt, the...

Red Storm usage model :Version 1.12.

Energy Technology Data Exchange (ETDEWEB)

Jefferson, Karen L.; Sturtevant, Judith E.

2005-12-01

Red Storm is an Advanced Simulation and Computing (ASC) funded massively parallel supercomputer located at Sandia National Laboratories (SNL). The Red Storm Usage Model (RSUM) documents the capabilities and the environment provided for the FY05 Tri-Lab Level II Limited Availability Red Storm User Environment Milestone and the FY05 SNL Level II Limited Availability Red Storm Platform Milestone. This document describes specific capabilities, tools, and procedures to support both local and remote users. The model is focused on the needs of the ASC user working in the secure computing environments at Los Alamos National Laboratory (LANL), Lawrence Livermore National Laboratory (LLNL), and SNL. Additionally, the Red Storm Usage Model maps the provided capabilities to the Tri-Lab ASC Computing Environment (ACE) requirements. The ACE requirements reflect the high performance computing requirements for the ASC community and have been updated in FY05 to reflect the community's needs. For each section of the RSUM, Appendix I maps the ACE requirements to the Limited Availability User Environment capabilities and includes a description of ACE requirements met and those requirements that are not met in that particular section. The Red Storm Usage Model, along with the ACE mappings, has been issued and vetted throughout the Tri-Lab community.

Multiple Evolutionary Selections Involved in Synonymous Codon Usages in the Streptococcus agalactiae Genome.

Science.gov (United States)

Ma, Yan-Ping; Ke, Hao; Liang, Zhi-Ling; Liu, Zhen-Xing; Hao, Le; Ma, Jiang-Yao; Li, Yu-Gu

2016-02-24

Streptococcus agalactiae is an important human and animal pathogen. To better understand the genetic features and evolution of S. agalactiae, multiple factors influencing synonymous codon usage patterns in S. agalactiae were analyzed in this study. A- and U-ending rich codons were used in S. agalactiae function genes through the overall codon usage analysis, indicating that Adenine (A)/Thymine (T) compositional constraints might contribute an important role to the synonymous codon usage pattern. The GC3% against the effective number of codon (ENC) value suggested that translational selection was the important factor for codon bias in the microorganism. Principal component analysis (PCA) showed that (i) mutational pressure was the most important factor in shaping codon usage of all open reading frames (ORFs) in the S. agalactiae genome; (ii) strand specific mutational bias was not capable of influencing the codon usage bias in the leading and lagging strands; and (iii) gene length was not the important factor in synonymous codon usage pattern in this organism. Additionally, the high correlation between tRNA adaptation index (tAI) value and codon adaptation index (CAI), frequency of optimal codons (Fop) value, reinforced the role of natural selection for efficient translation in S. agalactiae. Comparison of synonymous codon usage pattern between S. agalactiae and susceptible hosts (human and tilapia) showed that synonymous codon usage of S. agalactiae was independent of the synonymous codon usage of susceptible hosts. The study of codon usage in S. agalactiae may provide evidence about the molecular evolution of the bacterium and a greater understanding of evolutionary relationships between S. agalactiae and its hosts.

14 CFR 33.69 - Ignitions system.

Science.gov (United States)

2010-01-01

... STANDARDS: AIRCRAFT ENGINES Design and Construction; Turbine Aircraft Engines § 33.69 Ignitions system. Each..., except that only one igniter is required for fuel burning augmentation systems. [Amdt. 33-6, 39 FR 35466... 14 Aeronautics and Space 1 2010-01-01 2010-01-01 false Ignitions system. 33.69 Section 33.69...

19 CFR 4.69 - Shipping articles.

Science.gov (United States)

2010-04-01

... 19 Customs Duties 1 2010-04-01 2010-04-01 false Shipping articles. 4.69 Section 4.69 Customs... VESSELS IN FOREIGN AND DOMESTIC TRADES Foreign Clearances § 4.69 Shipping articles. No vessel of the U.S... officer, of the shipping articles agreements, including any seaman's allotment agreement, required by 46 U...

Genome-wide analysis of codon usage bias in four sequenced cotton species.

Science.gov (United States)

Wang, Liyuan; Xing, Huixian; Yuan, Yanchao; Wang, Xianlin; Saeed, Muhammad; Tao, Jincai; Feng, Wei; Zhang, Guihua; Song, Xianliang; Sun, Xuezhen

2018-01-01

Codon usage bias (CUB) is an important evolutionary feature in a genome which provides important information for studying organism evolution, gene function and exogenous gene expression. The CUB and its shaping factors in the nuclear genomes of four sequenced cotton species, G. arboreum (A2), G. raimondii (D5), G. hirsutum (AD1) and G. barbadense (AD2) were analyzed in the present study. The effective number of codons (ENC) analysis showed the CUB was weak in these four species and the four subgenomes of the two tetraploids. Codon composition analysis revealed these four species preferred to use pyrimidine-rich codons more frequently than purine-rich codons. Correlation analysis indicated that the base content at the third position of codons affect the degree of codon preference. PR2-bias plot and ENC-plot analyses revealed that the CUB patterns in these genomes and subgenomes were influenced by combined effects of translational selection, directional mutation and other factors. The translational selection (P2) analysis results, together with the non-significant correlation between GC12 and GC3, further revealed that translational selection played the dominant role over mutation pressure in the codon usage bias. Through relative synonymous codon usage (RSCU) analysis, we detected 25 high frequency codons preferred to end with T or A, and 31 low frequency codons inclined to end with C or G in these four species and four subgenomes. Finally, 19 to 26 optimal codons with 19 common ones were determined for each species and subgenomes, which preferred to end with A or T. We concluded that the codon usage bias was weak and the translation selection was the main shaping factor in nuclear genes of these four cotton genomes and four subgenomes.

Reactive glia promote development of CD103+ CD69+ CD8+ T-cells through programmed cell death-ligand 1 (PD-L1).

Science.gov (United States)

Prasad, Sujata; Hu, Shuxian; Sheng, Wen S; Chauhan, Priyanka; Lokensgard, James R

2018-06-01

Previous work from our laboratory has demonstrated in vivo persistence of CD103 + CD69 + brain resident memory CD8 + T-cells (bT RM ) following viral infection, and that the PD-1: PD-L1 pathway promotes development of these T RM cells within the brain. Although glial cells express low basal levels of PD-L1, its expression is upregulated upon IFN-γ-treatment, and they have been shown to modulate antiviral T-cell effector responses through the PD-1: PD-L1 pathway. We performed flow cytometric analysis of cells from co-cultures of mixed glia and CD8 + T-cells obtained from wild type mice to investigate the role of glial cells in the development of bT RM . In this study, we show that interactions between reactive glia and anti-CD3 Ab-stimulated CD8 + T-cells promote development of CD103 + CD69 + CD8 + T-cells through engagement of the PD-1: PD-L1 pathway. These studies used co-cultures of primary murine glial cells obtained from WT animals along with CD8 + T-cells obtained from either WT or PD-1 KO mice. We found that αCD3 Ab-stimulated CD8 + T-cells from WT animals increased expression of CD103 and CD69 when co-cultured with primary murine glial cells. In contrast, significantly reduced expression of CD103 and CD69 was observed using CD8 + T-cells from PD-1 KO mice. We also observed that reactive glia promoted high levels of CD127, a marker of memory precursor effector cells (MPEC), on CD69 + CD8 + T-cells, which promotes development of T RM cells. Interestingly, results obtained using T-cells from PD-1 KO animals showed significantly reduced expression of CD127 on CD69 + CD8 + cells. Additionally, blocking of glial PD-L1 resulted in decreased expression of CD103, along with reduced CD127 on CD69 + CD8 + T-cells. Taken together, these results demonstrate a role for activated glia in promoting development of bT RM through the PD-1: PD-L1 pathway. © 2018 The Authors. Immunity, Inflammation and Disease Published by John Wiley & Sons Ltd.

Compositional gradients in Gramineae genes

DEFF Research Database (Denmark)

Wong, Gane Ka-Shu; Wang, Jun; Tao, Lin

2002-01-01

In this study, we describe a property of Gramineae genes, and perhaps all monocot genes, that is not observed in eudicot genes. Along the direction of transcription, beginning at the junction of the 5'-UTR and the coding region, there are gradients in GC content, codon usage, and amino-acid usage...

Association between HIV-1 coreceptor usage and resistance to broadly neutralizing antibodies.

Science.gov (United States)

Pfeifer, Nico; Walter, Hauke; Lengauer, Thomas

2014-10-01

Recently discovered broadly neutralizing antibodies have revitalized hopes of developing a universal vaccine against HIV-1. Mainly responsible for new infections are variants only using CCR5 for cell entry, whereas CXCR4-using variants can become dominant in later infection stages. We performed a statistical analysis on two different previously published data sets. The first data set was a panel of 199 diverse HIV-1 isolates for which IC50 neutralization titers were determined for the broadly neutralizing antibodies VRC01, VRC-PG04, PG9, and PG16. The second data set contained env sequences of viral variants extracted from HIV-1-infected humanized mice treated with the antibody PGT128 and from untreated control mice. For the panel of 199 diverse HIV-1 isolates, we found a statistically significant association between viral resistance to PG9 and PG16 and CXCR4 coreceptor usage (P = 0.0011 and P = 0.0010, respectively). Our analysis of viral variants from HIV-1-infected humanized mice under treatment with the broadly neutralizing antibody PGT128 indicated that certain antibodies might drive a viral population toward developing CXCR4 coreceptor usage capability (P = 0.0011 for the comparison between PGT128 and control measurement). These analyses highlight the importance of accounting for a possible coreceptor usage bias pertaining to the effectiveness of an HIV vaccine and to passive antibody transfer as therapeutic approach.

MicroRNA-134 regulates lung cancer cell H69 growth and apoptosis by targeting WWOX gene and suppressing the ERK1/2 signaling pathway

International Nuclear Information System (INIS)

Chen, Tianjun; Gao, Fei; Feng, Sifang; Yang, Tian; Chen, Mingwei

2015-01-01

MicroRNAs have been shown to act as crucial modulators during carcinogenesis. Recent studies have implied that miR-134 expression associated with epithelial-to-mesenchymal transition phenotype and invasive potential of NSCLC cells. Our study investigated the pathogenic implications of miR-134 in small cell lung cancer (SCLC). Overexpression or inhibition MiR-134 expression by miR-134 mimics or miR-134 inhibitors (anti-miR-134) in SCLC cell lines was detected using qRT-PCR. Lactate dehydrogenase (LDH) assay, MTT assays and flow cytometry were performed in order to clarify the growth and apoptosis of SCLC cells which had been transfected with miR-134 mimics or anti-miR-134. WWOX expression in H69 cells was detected by qRT-PCR and western blot, respectively. The results showed that overexpression miR-134 was significantly promoting SCLC cells growth and inhibit its apoptosis. In addition, reduced miR-134 expression was significantly correlated with cell growth inhibition and apoptosis promotion. Furthermore, transfection of miR-134 mimics into the SCLC cells markedly down-regulated the level of WWOX, whereas, anti-miR-134 up-regulated WWOX expression. We also found that overexpression WWOX attenuate miR-134 induced H69 cells growth, and promote cell apoptosis. Moreover, miR-134 promoted cell proliferation and inhibit apoptosis via the activation of ERK1/2 pathway. These findings suggest that miR-134 may be an ideal diagnostic and prognostic marker, and may be attributed to the molecular therapy of SCLC. - Highlights: • MiR-134 play roles in small cell lung cancer cell growth and apoptosis. • MiR-134 negative regulated the level of WWOX in H69 cells. • WWOX overexpression attenuate miR-134 induced H69 cells growth. • MiR-134 promotes cell growth via the activation of ERK1/2 pathway

Differences in smartphone usage

DEFF Research Database (Denmark)

Gustarini, Mattia; Scipioni, Marcello Paolo; Fanourakis, Marios

2016-01-01

We analyze the users’ intimacy to investigate the differences in smartphone usage, considering the user’s location and number and kind of people physically around the user. With a first user study we (1) validate the intimacy concept, (2) evaluate its correlation to smartphone usage features and ...

Usage of removable partial dentures in Saudi male patients after 1 year telephone interview

Science.gov (United States)

Akeel, Riyadh

2010-01-01

Objective The success of removable partial dentures (RPDs) is partly dependent on patients’ acceptance and compliance in using them. The purpose of this study was to describe the usage of removable partial dentures (RPDs) by patients 1 year after insertion and to evaluate the factors that influence their denture usage. Methods Forty-seven patients who received 75 new RPDs at the undergraduate clinic of College of Dentistry, King Saud University, were contacted by telephone 1 year later for an interview. The questions covered denture usage, patient’s satisfaction and reasons for non-use. Results Results showed that 36% of patients discarded or occasionally used their RPDs. There was no significant association between denture usage and RPD experience, location or Kennedy classification. A significantly more RPD rejection was found when it was opposed by natural teeth or complete denture. The most quoted reason for RPD rejection was pain and discomfort. Conclusion Despite the short follow-up period, RPDs were poorly accepted by patients treated by undergraduate students. PMID:23960487

Association of arginine vasopressin receptor 1a gene polymorphisms with hepatorenal syndrome

International Nuclear Information System (INIS)

Wang, C.; Luo, X.; Ye, J.; Liu, S.; Miu, L.; Bao, J.; Wang, F.; Yu, Z.

2017-01-01

To assess the association of arginine vasopressin receptor 1a gene single nucleotide polymorphisms with type I hepatorenal syndrome. Methods: The case-control study was conducted at the Hangzhou City Xixi Hospital, Hangzhou, China, from January 2012 to June 2014, and comprised patients with type I hepatorenal syndrome and individuals with cirrhosis who acted as the control group. Arginine vasopressin receptor 1a gene rs113481894 locus single nucleotide polymorphisms were analysed by high-resolution melting methods. Statistical analysis was performed using SPSS 17. Results: Of the 60 participants, 28(46.7%) were in the hepatorenal syndrome group and 32(53.3%) were controls. The mean age was 42.21+-11.30years in the hepatorenal syndrome group and 43.69+-12.60 in the control group (p=0.64). Mean total bilirubin, albumin and prothrombin activity levels were 154.76+-51.58, 49.30+-24.67 and 33.42+-3.69 in the hepatorenal syndrome group compared to 181.26+-64.46, 41.78+-17.52 and 32.98+-4.81 among controls (p=0.09, p=0.18 and p=0.70). Statistically significant differences were found in the distributions of arginine vasopressin receptor 1a gene rs113481894 locus T allele between type I hepatorenal syndrome patients and the control group (odds ratio= 2.230; p= 0.040). Conclusion: T allele located at arginine vasopressin receptor 1a receptor promoter rs113481894 locus may be associated with the pathogenesis of type I hepatorenal syndrome. (author)

10 CFR 39.69 - Radioactive contamination control.

Science.gov (United States)

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Radioactive contamination control. 39.69 Section 39.69... Radiation Safety Requirements § 39.69 Radioactive contamination control. (a) If the licensee detects evidence that a sealed source has ruptured or licensed materials have caused contamination, the licensee...

Genetic architecture of HIV-1 genes circulating in north India & their functional implications.

Science.gov (United States)

Neogi, Ujjwal; Sood, Vikas; Ronsard, Larence; Singh, Jyotsna; Lata, Sneh; Ramachandran, V G; Das, S; Wanchu, Ajay; Banerjea, Akhil C

2011-12-01

This review presents data on genetic and functional analysis of some of the HIV-1 genes derived from HIV-1 infected individuals from north India (Delhi, Punjab and Chandigarh). We found evidence of novel B/C recombinants in HIV-1 LTR region showing relatedness to China/Myanmar with 3 copies of Nfκb sites; B/C/D mosaic genomes for HIV-1 Vpr and novel B/C Tat. We reported appearance of a complex recombinant form CRF_02AG of HIV-1 envelope sequences which is predominantly found in Central/Western Africa. Also one Indian HIV-1 envelope subtype C sequence suggested exclusive CXCR4 co-receptor usage. This extensive recombination, which is observed in about 10 per cent HIV-1 infected individuals in the Vpr genes, resulted in remarkably altered functions when compared with prototype subtype B Vpr. The Vpu C was found to be more potent in causing apoptosis when compared with Vpu B when analyzed for subG1 DNA content. The functional implications of these changes as well as in other genes of HIV-1 are discussed in detail with possible implications for subtype-specific pathogenesis highlighted.

Comparative investigation of the various determinants that influence the codon and amino acid usage patterns in the genus Bifidobacterium.

Science.gov (United States)

Roy, Ayan; Mukhopadhyay, Subhasish; Sarkar, Indrani; Sen, Arnab

2015-06-01

Various strains of the genus Bifidobacterium are crucial members of the human, animal and insect gut, associated with beneficial probiotic activities. An extensive analysis on codon and amino acid usage of the GC rich genus Bifidobacterium has been executed in the present study. Multivariate statistical analysis revealed a coupled effect of GC compositional constraint and natural selection for translational efficiency to be operative in producing the observed codon usage variations. Gene expression level was inferred to be the most crucial factor governing the codon usage patterns. Amino acid usage was found to be influenced significantly by hydrophobic and aromatic character of the encoded proteins. Gene expressivity and protein energetic cost also had considerable impact on the differential mode of amino acid usage. The genus was found to strictly obey the cost-minimization hypothesis as was reflected from the amino acid usage patterns of the potential highly expressed gene products. Evolutionary analysis revealed that the highly expressed genes were candidates to extreme evolutionary selection pressure and indicated a high degree of conservation at the proteomic level. Interestingly, the complimentary strands of replication appeared to evolve under similar evolutionary constraints which might be addressed as a consequence of absence of replicational selection and lack of strand-specific asymmetry among the members of the genus. Thus, the present endeavor confers considerable know-how pertaining to the codon and amino acid usage intricacies in Bifidobacterium and might prove handy for further scientific investigations associated with the concerned domain.

47 CFR 69.120 - Line information database.

Science.gov (United States)

2010-10-01

... 47 Telecommunication 3 2010-10-01 2010-10-01 false Line information database. 69.120 Section 69...) ACCESS CHARGES Computation of Charges § 69.120 Line information database. (a) A charge that is expressed... from a local exchange carrier database to recover the costs of: (1) The transmission facilities between...

Alternative promoter usage generates novel shorter MAPT mRNA transcripts in Alzheimer's disease and progressive supranuclear palsy brains.

Science.gov (United States)

Huin, Vincent; Buée, Luc; Behal, Hélène; Labreuche, Julien; Sablonnière, Bernard; Dhaenens, Claire-Marie

2017-10-03

Alternative promoter usage is an important mechanism for transcriptome diversity and the regulation of gene expression. Indeed, this alternative usage may influence tissue/subcellular specificity, protein translation and function of the proteins. The existence of an alternative promoter for MAPT gene was considered for a long time to explain differential tissue specificity and differential response to transcription and growth factors between mRNA transcripts. The alternative promoter usage could explain partly the different tau proteins expression patterns observed in tauopathies. Here, we report on our discovery of a functional alternative promoter for MAPT, located upstream of the gene's second exon (exon 1). By analyzing genome databases and brain tissue from control individuals and patients with Alzheimer's disease or progressive supranuclear palsy, we identified novel shorter transcripts derived from this alternative promoter. These transcripts are increased in patients' brain tissue as assessed by 5'RACE-PCR and qPCR. We suggest that these new MAPT isoforms can be translated into normal or amino-terminal-truncated tau proteins. We further suggest that activation of MAPT's alternative promoter under pathological conditions leads to the production of truncated proteins, changes in protein localization and function, and thus neurodegeneration.

Carboxylesterase 1 genes

DEFF Research Database (Denmark)

Rasmussen, Henrik Berg; Madsen, Majbritt Busk

2018-01-01

The carboxylesterase 1 gene (CES1) encodes a hydrolase that metabolizes commonly used drugs. The CES1-related pseudogene, carboxylesterase 1 pseudogene 1 (CES1P1), has been implicated in gene exchange with CES1 and in the formation of hybrid genes including the carboxylesterase 1A2 gene (CES1A2...

Gaming Device Usage Patterns Predict Internet Gaming Disorder: Comparison across Different Gaming Device Usage Patterns

OpenAIRE

Soo-Hyun Paik; Hyun Cho; Ji-Won Chun; Jo-Eun Jeong; Dai-Jin Kim

2017-01-01

Gaming behaviors have been significantly influenced by smartphones. This study was designed to explore gaming behaviors and clinical characteristics across different gaming device usage patterns and the role of the patterns on Internet gaming disorder (IGD). Responders of an online survey regarding smartphone and online game usage were classified by different gaming device usage patterns: (1) individuals who played only computer games; (2) individuals who played computer games more than smart...

G-protein inwardly rectifying potassium channel 1 (GIRK 1) gene expression correlates with tumor progression in non-small cell lung cancer

International Nuclear Information System (INIS)

Takanami, Iwao; Inoue, Yoshimasa; Gika, Masatoshi

2004-01-01

G-protein inwardly rectifying potassium channel 1 (GIRK1) is thought to play a role in cell proliferation in cancer, and GIRK1 gene expression level may define a more aggressive phenotype. We detected GIRK1 expression in tissue specimens from patients with non-small cell lung cancers (NSCLCs) and assessed their clinical characteristics. Using reverse transcription-polymerase chain reaction (RT-PCR) analyses, we quantified the expression of GIRK1 in 72 patients with NSCLCs to investigate the relationship between GIRK1 expression and clinicopathologic factors and prognosis. In 72 NSCLC patients, 50 (69%) samples were evaluated as having high GIRK1 gene expression, and 22 (31%) were evaluated as having low GIRK1 gene expression. GIRK1 gene expression was significantly associated with lymph node metastasis, stage (p = 0.0194 for lymph node metastasis; p = 0.0207 for stage). The overall and stage I survival rates for patients with high GIRK1 gene expressed tumors was significantly worse than for those individuals whose tumors had low GIRK1 expression (p = 0.0004 for the overall group; p = 0.0376 for stage I). These data indicate that GIRK1 may contribute to tumor progression and GIRK1 gene expression can serve as a useful prognostic marker in the overall and stage I NSCLCs

Comparative evolutionary genomics of Corynebacterium with special reference to codon and amino acid usage diversities.

Science.gov (United States)

Pal, Shilpee; Sarkar, Indrani; Roy, Ayan; Mohapatra, Pradeep K Das; Mondal, Keshab C; Sen, Arnab

2018-02-01

The present study has been aimed to the comparative analysis of high GC composition containing Corynebacterium genomes and their evolutionary study by exploring codon and amino acid usage patterns. Phylogenetic study by MLSA approach, indel analysis and BLAST matrix differentiated Corynebacterium species in pathogenic and non-pathogenic clusters. Correspondence analysis on synonymous codon usage reveals that, gene length, optimal codon frequencies and tRNA abundance affect the gene expression of Corynebacterium. Most of the optimal codons as well as translationally optimal codons are C ending i.e. RNY (R-purine, N-any nucleotide base, and Y-pyrimidine) and reveal translational selection pressure on codon bias of Corynebacterium. Amino acid usage is affected by hydrophobicity, aromaticity, protein energy cost, etc. Highly expressed genes followed the cost minimization hypothesis and are less diverged at their synonymous positions of codons. Functional analysis of core genes shows significant difference in pathogenic and non-pathogenic Corynebacterium. The study reveals close relationship between non-pathogenic and opportunistic pathogenic Corynebaterium as well as between molecular evolution and survival niches of the organism.

24 CFR 17.69 - Accounting control.

Science.gov (United States)

2010-04-01

... 24 Housing and Urban Development 1 2010-04-01 2010-04-01 false Accounting control. 17.69 Section... § 17.69 Accounting control. Each office and the Department Claims Officer shall process all claims collections through the appropriate accounting office and report the collection, compromise, suspension and...

Genome-wide comparative analysis of codon usage bias and codon context patterns among cyanobacterial genomes.

Science.gov (United States)

Prabha, Ratna; Singh, Dhananjaya P; Sinha, Swati; Ahmad, Khurshid; Rai, Anil

2017-04-01

With the increasing accumulation of genomic sequence information of prokaryotes, the study of codon usage bias has gained renewed attention. The purpose of this study was to examine codon selection pattern within and across cyanobacterial species belonging to diverse taxonomic orders and habitats. We performed detailed comparative analysis of cyanobacterial genomes with respect to codon bias. Our analysis reflects that in cyanobacterial genomes, A- and/or T-ending codons were used predominantly in the genes whereas G- and/or C-ending codons were largely avoided. Variation in the codon context usage of cyanobacterial genes corresponded to the clustering of cyanobacteria as per their GC content. Analysis of codon adaptation index (CAI) and synonymous codon usage order (SCUO) revealed that majority of genes are associated with low codon bias. Codon selection pattern in cyanobacterial genomes reflected compositional constraints as major influencing factor. It is also identified that although, mutational constraint may play some role in affecting codon usage bias in cyanobacteria, compositional constraint in terms of genomic GC composition coupled with environmental factors affected codon selection pattern in cyanobacterial genomes. Copyright © 2016 Elsevier B.V. All rights reserved.

Feasibility of sodium/iodide symporter gene as a new imaging reporter gene: comparison with HSV1-tk

International Nuclear Information System (INIS)

Shin, Jae Hoon; Chung, June-Key; Lee, Yong Jin; Kim, Kwang Il; Kang, Joo Hyun; Jeong, Jae Min; Lee, Dong Soo; Kim, Chul Woo; Lee, Myung Chul

2004-01-01

Positron emission tomography (PET) imaging reporter genes, such as HSV1-tk and D 2 receptor genes, make it possible to visualise gene expression non-invasively and repetitively in vivo. However, these systems require the synthesis of complicated substrates and the availability of expensive PET equipment. Expression of the sodium/iodide symporter (NIS) gene can be easily monitored with radioiodines and technetium-99m using a gamma camera. To evaluate the possibility of using NIS as an imaging reporter gene, we compared its characteristics with those of the conventional HSV1-tk gene. The CM cell line was made by transfecting the HSV1-tk gene into CT-26 (mouse colon carcinoma cell line). The CTN and CMN cell lines were then made by transfecting the NIS gene into CT-26 and CM. We measured the uptake of iodine-125 iodovinyldeoxyuridine ([ 125 I]IVDU) and 125 I to evaluate the expression of the HSV1-tk and NIS genes, respectively. Each cell line was injected into four flank sites in Balb/c mice. The biodistribution study was performed after intravenously injecting [ 125 I]IVDU and 131 I, and 131 I scintigraphy was performed for the evaluation of NIS expression. In vitro studies indicated that CTN and CMN had 40- to 79-fold and 150- to 256-fold higher uptake of 125 I than CT-26 and CM, respectively. Furthermore, CM and CMN showed 57- to 69-fold higher uptake of [ 125 I]IVDU than CT-26 and CTN. NIS gene expression and 125 I accumulation were found to be directly correlated (R 2 =0.923), as were HSV1-tk gene expression and [ 125 I]IVDU accumulation (R 2 =0.956). Calculated signal per unit NIS and HSV1-tk mRNA expression was 23,240±3,755 cpm and 34,039±5,346 cpm, respectively. In vivo study indicated that CTN and CMN had 2.3- and 5.8-fold higher uptake of 131 I than CT-26 and CM, and 1.8- and 3.5-fold higher uptake of [ 125 I]IVDU than CT-26 and CTN. Scintigraphy using 131 I easily visualised CTN and CMN tumours. In conclusion, the NIS gene may be viewed as an imaging

Association of ATP-Binding Cassette Transporter A1 Gene Polymorphisms in Type 2 Diabetes Mellitus among Malaysians

Directory of Open Access Journals (Sweden)

Polin Haghvirdizadeh

2015-01-01

Full Text Available Background. Type 2 diabetes mellitus (T2DM is a complex polygenic disorder characterized by impaired insulin resistance, insulin secretion, and dysregulation of lipid and protein metabolism with environmental and genetic factors. ATP-binding cassette transporter A1 (ABCA1 gene polymorphisms are reported as the one of the genetic risk factors for T2DM in various populations with conflicting results. This study was conducted based on PCR-HRM to determine the frequency of ABCA1 gene by rs2230806 (R219K, rs1800977 (C69T, and rs9282541 (R230C polymorphisms Malaysian subjects. Methods. A total of 164 T2DM and 165 controls were recruited and their genotypes for ABCA1 gene polymorphisms were determined based on the real time high resolution melting analysis. Results. There was a significant difference between the subjects in terms of age, BMI, FPG, HbA1c, HDL, LDL, and TG P<0.05. There was a significant association between HOM of R219K P=0.005, among Malaysian subjects; moreover, allele frequency revealed the significant difference in A allele of R219K P=0.003. But, there was no significant difference in genotypic and allelic frequencies of C69T and R230C polymorphism. Conclusion. R219K polymorphism of ABCA1 gene can be considered as a genetic risk factor for T2DM subjects among Malaysians.

In vivo evolution of HIV-1 co-receptor usage and sensitivity to chemokine-mediated suppression.

Science.gov (United States)

Scarlatti, G; Tresoldi, E; Björndal, A; Fredriksson, R; Colognesi, C; Deng, H K; Malnati, M S; Plebani, A; Siccardi, A G; Littman, D R; Fenyö, E M; Lusso, P

1997-11-01

Following the identification of the C-C chemokines RANTES, MIP-1alpha and MIP-1beta as major human immunodeficiency virus (HIV)-suppressive factors produced by CD8+ T cells, several chemokine receptors were found to serve as membrane co-receptors for primate immunodeficiency lentiretroviruses. The two most widely used co-receptors thus far recognized, CCR5 and CXCR4, are expressed by both activated T lymphocytes and mononuclear phagocytes. CCR5, a specific RANTES, MIP-1alpha and MIP-1 receptor, is used preferentially by non-MT2-tropic HIV-1 and HIV-2 strains and by simian immunodeficiency virus (SIV), whereas CXCR4, a receptor for the C-X-C chemokine SDF-1, is used by MT2-tropic HIV-1 and HIV-2, but not by SIV. Other receptors with a more restricted cellular distribution, such as CCR2b, CCR3 and STRL33, can also function as co-receptors for selected viral isolates. The third variable region (V3) of the gp120 envelope glycoprotein of HIV-1 has been fingered as a critical determinant of the co-receptor choice. Here, we document a consistent pattern of evolution of viral co-receptor usage and sensitivity to chemokine-mediated suppression in a longitudinal follow-up of children with progressive HIV-1 infection. Viral isolates obtained during the asymptomatic stages generally used only CCR5 as a co-receptor and were inhibited by RANTES, MIP-1alpha and MIP-1beta, but not by SDF-1. By contrast, the majority of the isolates derived after the progression of the disease were resistant to C-C chemokines, having acquired the ability to use CXCR4 and, in some cases, CCR3, while gradually losing CCR5 usage. Surprisingly, most of these isolates were also insensitive to SDF-1, even when used in combination with RANTES. An early acquisition of CXCR4 usage predicted a poor prognosis. In children who progressed to AIDS without a shift to CXCR4 usage, all the sequential isolates were CCR5-dependent but showed a reduced sensitivity to C-C chemokines. Discrete changes in the V3 domain

Codon usage determines translation rate in Escherichia coli

DEFF Research Database (Denmark)

Sørensen, Michael Askvad; Kurland, C G; Pedersen, Steen

1989-01-01

We wish to determine whether differences in translation rate are correlated with differences in codon usage or with differences in mRNA secondary structure. We therefore inserted a small DNA fragment in the lacZ gene either directly or flanked by a few frame-shifting bases, leaving the reading fr...

METEOR v1.0 - A usage example

International Nuclear Information System (INIS)

Palomo, E.

1994-01-01

This script describes a detailed example of the use of the software package METEOR for statistical analysis of meteorological data series. A real spanish meteorological data set is chosen to show the capabilities of METEOR. Output files and resultant plots provided of their interpretations are compiled in three appendixes. The original version of METEOR have been developed by Ph. D.Elena Palomo, CIEMAT-IER, GIASE. It is built by linking programs and routines written in FORTRAN 77 and it adds the graphical capabilities of GNUPLOT. The shape of this toolbox was designed following the criteria of modularity, flexibility and agility criteria. All the input, output and analysis options are structured in three main menus: i) the first is aimed to evaluate the quality of the data set; ii) the second is aimed for pre-processing of the data; and iii) the third is aimed towards the statistical analyses and for creating the graphical outputs. Actually the information about METEOR is constituted by three documents written is spanish: 1) METEOR v1.0: User's guide; 2) METEOR v1.0: A usage example; 3) METEOR v1 .0: Design and structure of the software package. (Author)

13 CFR 115.69 - Imminent Breach.

Science.gov (United States)

2010-01-01

... an Imminent Breach of the terms of a Contract covered by an SBA guaranteed bond. The PSB Surety does... 13 Business Credit and Assistance 1 2010-01-01 2010-01-01 false Imminent Breach. 115.69 Section... Surety Bond (PSB) Guarantees § 115.69 Imminent Breach. (a) No prior approval requirement. SBA will...

Immersion Suit Usage Within the RAAF

Science.gov (United States)

1992-01-01

IMMERSION SUIT USED UVIC QDIS HOLDINGS 202. in 12 Sizes, held by ALSS 492SQN REQUIREMENTS No comment USAGE POLICY REFERENCE DIRAF) AAP 7215.004-1 (P3C...held by ALSS 492SQN. REQUIREMENTS No comment ISACE POLICY REFERENCE DIIAF) AAP 7215.004-1 (P3C Flight Manual) RAAF Supplement No 92 USAGE POUICY UVIC...TYPE P3C REFERENCE Telecon FLTLT Toft I I SQNfRESO AVMED Dated 22 Mar 91 IMMERSION SUIT USED UVIC QDIS HOLDINGS No comment REQUIREMENTS No comment USAGE

Codon usage bias analysis for the coding sequences of Camellia ...

African Journals Online (AJOL)

sunny t

2016-02-24

Feb 24, 2016 ... suggested that codon usage bias is driven by selection, particularly for .... For example, as mentioned above, highly expressed genes tend to use fewer ... directional codon bias measure effective number of codons (ENc) was ...

46 CFR 5.69 - Evidence of criminal liability.

Science.gov (United States)

2010-10-01

... INVESTIGATION REGULATIONS-PERSONNEL ACTION Statement of Policy and Interpretation § 5.69 Evidence of criminal liability. Evidence of criminal liability discovered during an investigation or hearing conducted pursuant... 46 Shipping 1 2010-10-01 2010-10-01 false Evidence of criminal liability. 5.69 Section 5.69...

Ultra-High Resolution Orbit Determination of (486958) 2014 MU69: Predicting an Occultation with 1% of an Orbit

Science.gov (United States)

Porter, Simon Bernard; Buie, Marc W.; Spencer, John R.; Folkner, William; Parker, Alex; Zangari, Amanda Marie; Verbiscer, Anne J.; Benecchi, Susan; Stern, S. Alan; Terrell, Dirk; Soto, Alejandro; Tamblyn, Peter; Wasserman, Lawrence H.; Young, Eliot F.; New Horizons MU69 Occultation Team

2017-10-01

In November 2015, the NASA New Horizons spacecraft burned its thrusters to intercept the cold classical Kuiper Belt Object (486958) 2014 MU69. Then, on July 17, 2017, five small telescopes in Chubut Province, Argentina recorded a solid body occultation of MU69. Both these events required an orbital solution of unprecedented accuracy, as will the January 1, 2019 flyby of MU69 by New Horizons. This was especially difficult because there were no precoveries of MU69 prior to July 2014, it is in an extremely crowded field near the galactic core, and it is faint enough to only be reliably detected by Hubble Space Telescope’s Wide Field Camera 3 (WFC3). To accomplish this, we performed an extremely detailed analysis of 237 WFC3 images, down to the subpixel distortion level, in order to produce individual probability distribution functions (PDFs) for the position of MU69 in each WFC3 image. We registered each WFC3 image against a pre-release version of the Gaia DR2 catalog, which produced even smaller residuals than the now-released DR1. We then combined these WFC3+Gaia PDFs with a high-precision few-body numerical integrator and a Monte Carlo Markov Chain (MCMC) sampler to produce a state vector PDF for MU69 at defined epoch. Propagating those state vectors from the epoch produces an instantaneous positional cloud for MU69 at any given time. This positional cloud was then directly translated into a shadow path uncertainty cloud in order to plan the MU69 occultation campaign. We will describe this process of fully propagating errors from WFC3 images to telescope sites on the ground, and also describe refinements for future guiding of New Horizons to its encounter with MU69. We thank NASA, Hubble, Gaia, CONAE, the city of Comodoro Rivadavia, and the government of Argentina for their assistance and support of the MU69 occultation campaign.

10 CFR 34.69 - Records of quarterly inventory.

Science.gov (United States)

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Records of quarterly inventory. 34.69 Section 34.69 Energy... INDUSTRIAL RADIOGRAPHIC OPERATIONS Recordkeeping Requirements § 34.69 Records of quarterly inventory. (a) Each licensee shall maintain records of the quarterly inventory of sealed sources and of devices...

Mutational analysis of COL1A1 and COL1A2 genes among Estonian osteogenesis imperfecta patients.

Science.gov (United States)

Zhytnik, Lidiia; Maasalu, Katre; Reimann, Ene; Prans, Ele; Kõks, Sulev; Märtson, Aare

2017-08-15

Osteogenesis imperfecta (OI) is a rare bone disorder. In 90% of cases, OI is caused by mutations in the COL1A1/2 genes, which code procollagen α1 and α2 chains. The main aim of the current research was to identify the mutational spectrum of COL1A1/2 genes in Estonian patients. The small population size of Estonia provides a unique chance to explore the collagen I mutational profile of 100% of OI families in the country. We performed mutational analysis of peripheral blood gDNA of 30 unrelated Estonian OI patients using Sanger sequencing of COL1A1 and COL1A2 genes, including all intron-exon junctions and 5'UTR and 3'UTR regions, to identify causative OI mutations. We identified COL1A1/2 mutations in 86.67% of patients (26/30). 76.92% of discovered mutations were located in the COL1A1 (n = 20) and 23.08% in the COL1A2 (n = 6) gene. Half of the COL1A1/2 mutations appeared to be novel. The percentage of quantitative COL1A1/2 mutations was 69.23%. Glycine substitution with serine was the most prevalent among missense mutations. All qualitative mutations were situated in the chain domain of pro-α1/2 chains. Our study shows that among the Estonian OI population, the range of collagen I mutations is quite high, which agrees with other described OI cohorts of Northern Europe. The Estonian OI cohort differs due to the high number of quantitative variants and simple missense variants, which are mostly Gly to Ser substitutions and do not extend the chain domain of COL1A1/2 products.

Expression and function of the zinc finger transcription factor Sp6-9 in the spider Parasteatoda tepidariorum.

Science.gov (United States)

Königsmann, Tatiana; Turetzek, Natascha; Pechmann, Matthias; Prpic, Nikola-Michael

2017-11-01

Zinc finger transcription factors of the Sp6-9 group are evolutionarily conserved in all metazoans and have important functions in, e.g., limb formation and heart development. The function of Sp6-9-related genes has been studied in a number of vertebrates and invertebrates, but data from chelicerates (spiders and allies) was lacking so far. We have isolated the ortholog of Sp6-9 from the common house spider Parasteatoda tepidariorum and the cellar spider Pholcus phalangioides. We show that the Sp6-9 gene in these spider species is expressed in the developing appendages thus suggesting a conserved role in limb formation. Indeed, RNAi with Sp6-9 in P. tepidariorum leads not only to strong limb defects, but also to the loss of body segments and head defects in more strongly affected animals. Together with a new expression domain in the early embryo, these data suggest that Sp6-9 has a dual role P. tepidariorum. The early role in head and body segment formation is not known from other arthropods, but the role in limb formation is evolutionarily highly conserved.

Prevailing clone (ST69) of Vibrio cholerae O139 in India over 10 years.

Science.gov (United States)

Anandan, Shalini; Devanga Ragupathi, Naveen Kumar; Muthuirulandi Sethuvel, Dhiviya Prabaa; Thangamani, Suji; Veeraraghavan, Balaji

2017-01-01

Vibrio cholerae is responsible for the cause of severe life-threatening infection known as cholera. The study aimed to analyze the genetic make-up of V. cholerae O139 isolates from India and compare its phylogeny with the global strains. The genome data revealed that all isolates were of same sequence type (ST69) which belongs to seventh pandemic clone, with same virulence gene profile and, antimicrobial resistance gene profile except for two isolates. No known CRISPR repeats were identified in any of these isolates. Three different phages were identified among the isolates. All the isolates were found to harbour int SXT and seventh pandemic-specific gene (VC2346). Results from this study enhance our understanding on the persistence of ST69 V. cholerae O139 over 20 years.

Comparative studies on codon usage pattern of chloroplasts and ...

Indian Academy of Sciences (India)

Unknown

different genomic organization and mutation pressures in nuclear and chloroplast genes. The results of Nc-plots and neutrality plots ... As an important organelle of plants, the chloroplast has its own genomic environment and ... leading to the suggestion that the translation mechanism and patterns of codon usage in ...

Systematic Search for Gene-Gene Interaction Effect on Prostate Cancer Risk

Science.gov (United States)

2013-07-01

Systematic Search for Gene-Gene Interaction 5a. CONTRACT NUMBER Effect on Prostate Cancer Risk 5b. GRANT NUMBER W81XWH-09-1-0488 5c. PROGRAM...Supported by this grant ) 1. Tao S, Wang Z, Feng J, Hsu FC, Jin G, Kin ST, Zhang Z, Gronberg H, Zheng, SL, Isaacs WB, XU J, Sun J. A Genome-Wide Search for...order interactions among estrogen- metabolism genes in sporadic breast cancer. Am J Hum Genet, 69, 138-47. 48. Marchini, J., Donnelly, P. and Cardon

Dek-can rearrangement in translocation (6;9)(p23;q34)

NARCIS (Netherlands)

Soekarman, D.; von Lindern, M.; van der Plas, D. C.; Selleri, L.; Bartram, C. R.; Martiat, P.; Culligan, D.; Padua, R. A.; Hasper-Voogt, K. P.; Hagemeijer, A.

1992-01-01

The translocation (6;9)(p23;q34) is mainly found in specific subtypes of acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). The diagnosis of this translocation is not easy since the cytogenetic change is quite subtle. The two genes involved in this translocation were recently isolated

Codon Usage Bias and Determining Forces in Taenia solium Genome.

Science.gov (United States)

Yang, Xing; Ma, Xusheng; Luo, Xuenong; Ling, Houjun; Zhang, Xichen; Cai, Xuepeng

2015-12-01

The tapeworm Taenia solium is an important human zoonotic parasite that causes great economic loss and also endangers public health. At present, an effective vaccine that will prevent infection and chemotherapy without any side effect remains to be developed. In this study, codon usage patterns in the T. solium genome were examined through 8,484 protein-coding genes. Neutrality analysis showed that T. solium had a narrow GC distribution, and a significant correlation was observed between GC12 and GC3. Examination of an NC (ENC vs GC3s)-plot showed a few genes on or close to the expected curve, but the majority of points with low-ENC (the effective number of codons) values were detected below the expected curve, suggesting that mutational bias plays a major role in shaping codon usage. The Parity Rule 2 plot (PR2) analysis showed that GC and AT were not used proportionally. We also identified 26 optimal codons in the T. solium genome, all of which ended with either a G or C residue. These optimal codons in the T. solium genome are likely consistent with tRNAs that are highly expressed in the cell, suggesting that mutational and translational selection forces are probably driving factors of codon usage bias in the T. solium genome.

Comparative analysis of codon usage bias and codon context patterns between dipteran and hymenopteran sequenced genomes.

Directory of Open Access Journals (Sweden)

Susanta K Behura

Full Text Available BACKGROUND: Codon bias is a phenomenon of non-uniform usage of codons whereas codon context generally refers to sequential pair of codons in a gene. Although genome sequencing of multiple species of dipteran and hymenopteran insects have been completed only a few of these species have been analyzed for codon usage bias. METHODS AND PRINCIPAL FINDINGS: Here, we use bioinformatics approaches to analyze codon usage bias and codon context patterns in a genome-wide manner among 15 dipteran and 7 hymenopteran insect species. Results show that GAA is the most frequent codon in the dipteran species whereas GAG is the most frequent codon in the hymenopteran species. Data reveals that codons ending with C or G are frequently used in the dipteran genomes whereas codons ending with A or T are frequently used in the hymenopteran genomes. Synonymous codon usage orders (SCUO vary within genomes in a pattern that seems to be distinct for each species. Based on comparison of 30 one-to-one orthologous genes among 17 species, the fruit fly Drosophila willistoni shows the least codon usage bias whereas the honey bee (Apis mellifera shows the highest bias. Analysis of codon context patterns of these insects shows that specific codons are frequently used as the 3'- and 5'-context of start and stop codons, respectively. CONCLUSIONS: Codon bias pattern is distinct between dipteran and hymenopteran insects. While codon bias is favored by high GC content of dipteran genomes, high AT content of genes favors biased usage of synonymous codons in the hymenopteran insects. Also, codon context patterns vary among these species largely according to their phylogeny.

Whole-genome sequencing of Bacillus velezensis LS69, a strain with a broad inhibitory spectrum against pathogenic bacteria.

Science.gov (United States)

Liu, Guoqiang; Kong, Yingying; Fan, Yajing; Geng, Ce; Peng, Donghai; Sun, Ming

2017-05-10

Bacillus velezensis LS69 was found to exhibit antagonistic activity against a diverse spectrum of pathogenic bacteria. It has one circular chromosome of 3,917,761bp with 3,643 open reading frames. Genome analysis identified ten gene clusters involved in nonribosomal synthesis of polyketides (macrolactin, bacillaene and difficidin), lipopeptides (surfactin, fengycin, bacilysin and iturin A) and bacteriocins (amylolysin and amylocyclicin). In addition, B. velezensis LS69 was found to contain a series of genes involved in enhancing plant growth and triggering plant immunity. Whole genome sequencing of Bacillus velezensis LS69 will provide a basis for elucidation of its biocontrol mechanisms and facilitate its applications in the future. Copyright © 2017 Elsevier B.V. All rights reserved.

Induction of CD69 expression by cagPAI-positive Helicobacter pylori infection

Institute of Scientific and Technical Information of China (English)

Naoki Mori; Chie Ishikawa; Masachika Senba

2011-01-01

AIM: To investigate and elucidate the molecular mech-anism that regulates inducible expression of CD69 by Helicobacter pylori (H. pylori ) infection.METHODS: The expression levels of CD69 in a T-cell line, Jurkat, primary human peripheral blood mononu-clear cells (PBMCs), and CD4+T cells, were assessed by immunohistochemistry, reverse transcription polymerase chain reaction, and flow cytometry. Activation of CD69 promoter was detected by reporter gene. Nuclear factor (NF)-κB activation in Jurkat cells infected with H. pylori was evaluated by electrophoretic mobility shift assay. The role of NF-κB signaling in H. pylori -induced CD69 expression was analyzed using inhibitors of NF-κB and dominant-negative mutants. The isogenic mutants with disrupted cag pathogenicity island ( cagPAI) and virD4 were used to elucidate the role of cagPAI-encoding type Ⅳ secretion system and CagA in CD69 expression.RESULTS: CD69 staining was detected in mucosal lymphocytes and macrophages in specimens of pa-tients with H. pylori -positive gastritis. Although cagPAI-positive H. pylori and an isogenic mutant of virD4 induced CD69 expression, an isogenic mutant of cag-PAI failed to induce this in Jurkat cells. H. pylori also induced CD69 expression in PBMCs and CD4+T cells. The activation of the CD69 promoter by H. pylori was mediated through NF-κB. Transfection of dominant-negative mutants of IκBs, IκB kinases, and NF-κB-inducing kinase inhibited H. pylori -induced CD69 activation. Inhibitors of NF-κB suppressed H. pylori -induced CD69 mRNA expression.CONCLUSION: The results suggest that H. pylori in-duces CD69 expression through the activation of NF-κB. cagPAI might be relevant in the induction of CD69 expression in T cells. CD69 in T cells may play a role in H. pylori -induced gastritis.

Codon usage bias: causative factors, quantification methods and genome-wide patterns: with emphasis on insect genomes.

Science.gov (United States)

Behura, Susanta K; Severson, David W

2013-02-01

Codon usage bias refers to the phenomenon where specific codons are used more often than other synonymous codons during translation of genes, the extent of which varies within and among species. Molecular evolutionary investigations suggest that codon bias is manifested as a result of balance between mutational and translational selection of such genes and that this phenomenon is widespread across species and may contribute to genome evolution in a significant manner. With the advent of whole-genome sequencing of numerous species, both prokaryotes and eukaryotes, genome-wide patterns of codon bias are emerging in different organisms. Various factors such as expression level, GC content, recombination rates, RNA stability, codon position, gene length and others (including environmental stress and population size) can influence codon usage bias within and among species. Moreover, there has been a continuous quest towards developing new concepts and tools to measure the extent of codon usage bias of genes. In this review, we outline the fundamental concepts of evolution of the genetic code, discuss various factors that may influence biased usage of synonymous codons and then outline different principles and methods of measurement of codon usage bias. Finally, we discuss selected studies performed using whole-genome sequences of different insect species to show how codon bias patterns vary within and among genomes. We conclude with generalized remarks on specific emerging aspects of codon bias studies and highlight the recent explosion of genome-sequencing efforts on arthropods (such as twelve Drosophila species, species of ants, honeybee, Nasonia and Anopheles mosquitoes as well as the recent launch of a genome-sequencing project involving 5000 insects and other arthropods) that may help us to understand better the evolution of codon bias and its biological significance. © 2012 The Authors. Biological Reviews © 2012 Cambridge Philosophical Society.

41 CFR 50-204.69 - Nitrous oxide.

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2010-07-01

... 41 Public Contracts and Property Management 1 2010-07-01 2010-07-01 true Nitrous oxide. 50-204.69..., Vapors, Fumes, Dusts, and Mists § 50-204.69 Nitrous oxide. The piped systems for the in-plant transfer and distribution of nitrous oxide shall be designed, installed, maintained, and operated in accordance...

Kalrn promoter usage and isoform expression respond to chronic cocaine exposure

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Ma Xin-Ming

2011-02-01

Full Text Available Abstract Background The long-term effects of cocaine on behavior are accompanied by structural changes in excitatory glutamatergic synapses onto the medium spiny neurons of the striatum. The Kalrn gene encodes several functionally distinct isoforms; these multidomain guanine nucleotide exchange factors (GEFs contain additional domains known to interact with phosphatidylinositides as well as with a number of different proteins. Through their activation of Rho proteins and their interactions with other proteins, the different Kalirin isoforms affect cytoskeletal organization. Chronic exposure of adult male rodents to cocaine increases levels of Kalirin 7 in the striatum. When exposed chronically to cocaine, mice lacking Kalirin 7, the major adult isoform, fail to show an increase in dendritic spine density in the nucleus accumbens, show diminished place preference for cocaine, and exhibit increased locomotor activity in response to cocaine. Results The use of alternate promoters and 3'-terminal exons of the mouse Kalrn gene were investigated using real-time quantitative polymerase chain reaction. While the two most distal full-length Kalrn promoters are used equally in the prefrontal cortex, the more proximal of these promoters accounts for most of the transcripts expressed in the nucleus accumbens. The 3'-terminal exon unique to the Kalirin 7 isoform accounts for a greater percentage of the Kalrn transcripts in prefrontal cortex than in nucleus accumbens. Western blot analyses confirmed these differences. Chronic cocaine treatment increases usage of the promoter encoding the Δ-Kalirin isoforms but does not alter full-length Kalirin promoter usage. Usage of the 3'-terminal exon unique to Kalirin 7 increases following chronic cocaine exposure. Conclusions Kalrn promoter and 3'-terminal exon utilization are region-specific. In the nucleus accumbens, cocaine-mediated alterations in promoter usage and 3'-terminal exon usage favor expression of

The early activation marker CD69 regulates the expression of chemokines and CD4 T cell accumulation in intestine.

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Katarina Radulovic

Full Text Available Migration of naïve and activated lymphocytes is regulated by the expression of various molecules such as chemokine receptors and ligands. CD69, the early activation marker of C-type lectin domain family, is also shown to regulate the lymphocyte migration by affecting their egress from the thymus and secondary lymphoid organs. Here, we aimed to investigate the role of CD69 in accumulation of CD4 T cells in intestine using murine models of inflammatory bowel disease. We found that genetic deletion of CD69 in mice increases the expression of the chemokines CCL-1, CXCL-10 and CCL-19 in CD4(+ T cells and/or CD4(- cells. Efficient in vitro migration of CD69-deficient CD4 T cells toward the chemokine stimuli was the result of increased expression and/or affinity of chemokine receptors. In vivo CD69(-/- CD4 T cells accumulate in the intestine in higher numbers than B6 CD4 T cells as observed in competitive homing assay, dextran sodium sulphate (DSS-induced colitis and antigen-specific transfer colitis. In DSS colitis CD69(-/- CD4 T cell accumulation in colonic lamina propria (cLP was associated with increased expression of CCL-1, CXCL-10 and CCL-19 genes. Furthermore, treatment of DSS-administrated CD69(-/- mice with the mixture of CCL-1, CXCL-10 and CCL-19 neutralizing Abs significantly decreased the histopathological signs of colitis. Transfer of OT-II×CD69(-/- CD45RB(high CD4 T cells into RAG(-/- hosts induced CD4 T cell accumulation in cLP. This study showed CD69 as negative regulator of inflammatory responses in intestine as it decreases the expression of chemotactic receptors and ligands and reduces the accumulation of CD4 T cells in cLP during colitis.

Permeability and giant magnetoimpedance in Co69Fe4.5X1.5Si10B15 (X=Cr, Mn, Ni) amorphous ribbons

International Nuclear Information System (INIS)

Byon, Kwang Seok; Yu, Seong-Cho; Kim, Cheol Gi

2001-01-01

The magnetoimpedance (MI) has been measured in the amorphous ribbons of the soft ferromagnetic alloy Co 69 Fe 4.5 X 1.5 Si 10 B 15 (X=Cr, Mn, Ni) as functions of frequency (f). For all of the three samples, at low frequency, f≤5MHz, the MI ratio increases with increasing frequency, but the MI ratio decreases at high frequency, f≥5MHz. The MI profiles are not changed at low frequency regions of f≤1MHz in the amorphous ribbons. The MI ratio at high frequency of f=5MHz becomes 57% in Co 69 Fe 4.5 Cr 1.5 Si 10 B 15 , but the MI ratio becomes 30% in Co 69 Fe 4.5 Mn 1.5 Si 10 B 15 and Co 69 Fe 4.5 Ni 1.5 Si 10 B 15 . The MI ratio at f=10MHz becomes 45% in Co 69 Fe 4.5 Cr 1.5 Si 10 B 15 and the MI ratio becomes 23% in Co 69 Fe 4.5 Mn 1.5 Si 10 B 15 and Co 69 Fe 4.5 Ni 1.5 Si 10 B 15 , respectively. The maximum values of field sensitivity are 2.7(X=Cr), 2.5(X=Mn), 2.2(X=Ni)%/Oe for f=5MHz. [copyright] 2001 American Institute of Physics

TET2 mutations in B cells of patients affected by angioimmunoblastic T-cell lymphoma.

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Schwartz, Friederike H; Cai, Qian; Fellmann, Eva; Hartmann, Sylvia; Mäyränpää, Mikko I; Karjalainen-Lindsberg, Marja-Liisa; Sundström, Christer; Scholtysik, René; Hansmann, Martin-Leo; Küppers, Ralf

2017-06-01

Angioimmunoblastic T-cell lymphomas (AITLs) frequently carry mutations in the TET2 and IDH2 genes. TET2 mutations represent early genetic lesions as they had already been detected in haematopoietic precursor cells of AITL patients. We show by analysis of whole-tissue sections and microdissected PD1 + cells that the frequency of TET2-mutated AITL is presumably even higher than reported (12/13 cases in our collection; 92%). In two-thirds of informative AITLs (6/9), a fraction of B cells was also TET2-mutated. Investigation of four AITLs by TET2 and IGHV gene sequencing of single microdissected B cells showed that between 10% and 60% of polyclonal B cells in AITL lymph nodes harboured the identical TET2 mutations of the respective T-cell lymphoma clone. Thus, TET2-mutated haematopoietic precursor cells in AITL patients not only give rise to the T-cell lymphoma but also generate a large population of mutated mature B cells. Future studies will show whether this is a reason why AITL patients frequently also develop B-cell lymphomas. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Usage Center

DEFF Research Database (Denmark)

Kleinaltenkamp, Michael; Plewa, Carolin; Gudergan, Siegfried

2017-01-01

Purpose: The purpose of this paper is to advance extant theorizing around resourceintegration by conceptualizing and delineating the notion of a usage center. Ausage center consists of a combination of interdependent actors that draw onresources across their individual usage processes to create v...

The multidrug resistance 1 gene Abcb1 in brain and placenta: comparative analysis in human and guinea pig.

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Pappas, Jane J; Petropoulos, Sophie; Suderman, Matthew; Iqbal, Majid; Moisiadis, Vasilis; Turecki, Gustavo; Matthews, Stephen G; Szyf, Moshe

2014-01-01

The Multidrug Resistance 1 (MDR1; alternatively ABCB1) gene product P-glycoprotein (P-gp), an ATP binding cassette transporter, extrudes multiple endogenous and exogenous substrates from the cell, playing an important role in normal physiology and xenobiotic distribution and bioavailability. To date, the predominant animal models used to investigate the role of P-gp have been the mouse and rat, which have two distinct genes, Abcb1a and Abcb1b. In contrast, the human has a single gene, ABCB1, for which only a single isoform has been validated. We and others have previously shown important differences between Abcb1a and Abcb1b, limiting the extrapolation from rodent findings to the human. Since the guinea pig has a relatively long gestation, hemomonochorial placentation and neuroanatomically mature offspring, it is more similar to the human, and may provide a more comparable model for investigating the regulation of P-gp in the brain and placenta, however, to date, the Abcb1 gene in the guinea pig remains to be characterized. The placenta and fetal brain are barrier sites that express P-gp and that play a critical role of protection of the fetus and the fetal brain from maternally administered drugs and other xenobiotics. Using RNA sequencing (RNA-seq), reverse transcription-polymerase chain reaction (RT-PCR) and quantitative PCR (QPCR) to sequence the expressed isoforms of guinea pig Abcb1, we demonstrate that like the human, the guinea pig genome contains one gene for Abcb1 but that it is expressed as at least three different isoforms via alternative splicing and alternate exon usage. Further, we demonstrate that these isoforms are more closely related to human than to rat or mouse isoforms. This striking, overall similarity and evolutionary relatedness between guinea pig Abcb1 and human ABCB1 indicate that the guinea pig represents a relevant animal model for investigating the function and regulation of P-gp in the placenta and brain.

Digging deeper: new gene order rearrangements and distinct patterns of codons usage in mitochondrial genomes among shrimps from the Axiidea, Gebiidea and Caridea (Crustacea: Decapoda

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Mun Hua Tan

2017-03-01

Full Text Available Background Whole mitochondrial DNA is being increasingly utilized for comparative genomic and phylogenetic studies at deep and shallow evolutionary levels for a range of taxonomic groups. Although mitogenome sequences are deposited at an increasing rate into public databases, their taxonomic representation is unequal across major taxonomic groups. In the case of decapod crustaceans, several infraorders, including Axiidea (ghost shrimps, sponge shrimps, and mud lobsters and Caridea (true shrimps are still under-represented, limiting comprehensive phylogenetic studies that utilize mitogenomic information. Methods Sequence reads from partial genome scans were generated using the Illumina MiSeq platform and mitogenome sequences were assembled from these low coverage reads. In addition to examining phylogenetic relationships within the three infraorders, Axiidea, Gebiidea, and Caridea, we also investigated the diversity and frequency of codon usage bias and mitogenome gene order rearrangements. Results We present new mitogenome sequences for five shrimp species from Australia that includes two ghost shrimps, Callianassa ceramica and Trypaea australiensis, along with three caridean shrimps, Macrobrachium bullatum, Alpheus lobidens, and Caridina cf. nilotica. Strong differences in codon usage were discovered among the three infraorders and significant gene order rearrangements were observed. While the gene order rearrangements are congruent with the inferred phylogenetic relationships and consistent with taxonomic classification, they are unevenly distributed within and among the three infraorders. Discussion Our findings suggest potential for mitogenome rearrangements to be useful phylogenetic markers for decapod crustaceans and at the same time raise important questions concerning the drivers of mitogenome evolution in different decapod crustacean lineages.

Difference between age-related macular degeneration and polypoidal choroidal vasculopathy in the hereditary contribution of the A69S variant of the age-related maculopathy susceptibility 2 gene (ARMS2).

Science.gov (United States)

Yanagisawa, Suiho; Kondo, Naoshi; Miki, Akiko; Matsumiya, Wataru; Kusuhara, Sentaro; Tsukahara, Yasutomo; Honda, Shigeru; Negi, Akira

2011-01-01

To investigate whether the A69S variant of the age-related maculopathy susceptibility 2 gene (ARMS2) has a different hereditary contribution in neovascular age-related macular degeneration (AMD) and polypoidal choroidal vasculopathy (PCV). We initially conducted a comparative genetic analysis of neovascular AMD and PCV, genotyping the ARMS2 A69S variant in 181 subjects with neovascular AMD, 198 subjects with PCV, and 203 controls in a Japanese population. Genotyping was conducted using TaqMan technology. Results were then integrated into a meta-analysis of previous studies representing an assessment of the association between the ARMS2 A69S variant and neovascular AMD and/or PCV, comprising a total of 3,828 subjects of Asian descent. The Q-statistic test was used to assess between-study heterogeneity. Summary odds ratios (ORs) and 95% confidence intervals (CIs) were estimated using a fixed effects model. The genetic effect of the A69S variant was stronger in neovascular AMD (allelic summary OR=3.09 [95% CI, 2.71-3.51], fixed effects parchitecture of this phenotypically heterogeneous disorder.

9 CFR 113.69 - Pasteurella Multocida Vaccine, Bovine.

Science.gov (United States)

2010-01-01

... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Pasteurella Multocida Vaccine, Bovine. 113.69 Section 113.69 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE... Animal and Plant Health Inspection Service. (4) A satisfactory challenge shall be evidenced in the...

Gaming Device Usage Patterns Predict Internet Gaming Disorder: Comparison across Different Gaming Device Usage Patterns

Science.gov (United States)

Cho, Hyun; Chun, Ji-Won; Jeong, Jo-Eun; Kim, Dai-Jin

2017-01-01

Gaming behaviors have been significantly influenced by smartphones. This study was designed to explore gaming behaviors and clinical characteristics across different gaming device usage patterns and the role of the patterns on Internet gaming disorder (IGD). Responders of an online survey regarding smartphone and online game usage were classified by different gaming device usage patterns: (1) individuals who played only computer games; (2) individuals who played computer games more than smartphone games; (3) individuals who played computer and smartphone games evenly; (4) individuals who played smartphone games more than computer games; (5) individuals who played only smartphone games. Data on demographics, gaming-related behaviors, and scales for Internet and smartphone addiction, depression, anxiety disorder, and substance use were collected. Combined users, especially those who played computer and smartphone games evenly, had higher prevalence of IGD, depression, anxiety disorder, and substance use disorder. These subjects were more prone to develop IGD than reference group (computer only gamers) (B = 0.457, odds ratio = 1.579). Smartphone only gamers had the lowest prevalence of IGD, spent the least time and money on gaming, and showed lowest scores of Internet and smartphone addiction. Our findings suggest that gaming device usage patterns may be associated with the occurrence, course, and prognosis of IGD. PMID:29206183

Gaming Device Usage Patterns Predict Internet Gaming Disorder: Comparison across Different Gaming Device Usage Patterns.

Science.gov (United States)

Paik, Soo-Hyun; Cho, Hyun; Chun, Ji-Won; Jeong, Jo-Eun; Kim, Dai-Jin

2017-12-05

Gaming behaviors have been significantly influenced by smartphones. This study was designed to explore gaming behaviors and clinical characteristics across different gaming device usage patterns and the role of the patterns on Internet gaming disorder (IGD). Responders of an online survey regarding smartphone and online game usage were classified by different gaming device usage patterns: (1) individuals who played only computer games; (2) individuals who played computer games more than smartphone games; (3) individuals who played computer and smartphone games evenly; (4) individuals who played smartphone games more than computer games; (5) individuals who played only smartphone games. Data on demographics, gaming-related behaviors, and scales for Internet and smartphone addiction, depression, anxiety disorder, and substance use were collected. Combined users, especially those who played computer and smartphone games evenly, had higher prevalence of IGD, depression, anxiety disorder, and substance use disorder. These subjects were more prone to develop IGD than reference group (computer only gamers) (B = 0.457, odds ratio = 1.579). Smartphone only gamers had the lowest prevalence of IGD, spent the least time and money on gaming, and showed lowest scores of Internet and smartphone addiction. Our findings suggest that gaming device usage patterns may be associated with the occurrence, course, and prognosis of IGD.

Gaming Device Usage Patterns Predict Internet Gaming Disorder: Comparison across Different Gaming Device Usage Patterns

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Soo-Hyun Paik

2017-12-01

Full Text Available Gaming behaviors have been significantly influenced by smartphones. This study was designed to explore gaming behaviors and clinical characteristics across different gaming device usage patterns and the role of the patterns on Internet gaming disorder (IGD. Responders of an online survey regarding smartphone and online game usage were classified by different gaming device usage patterns: (1 individuals who played only computer games; (2 individuals who played computer games more than smartphone games; (3 individuals who played computer and smartphone games evenly; (4 individuals who played smartphone games more than computer games; (5 individuals who played only smartphone games. Data on demographics, gaming-related behaviors, and scales for Internet and smartphone addiction, depression, anxiety disorder, and substance use were collected. Combined users, especially those who played computer and smartphone games evenly, had higher prevalence of IGD, depression, anxiety disorder, and substance use disorder. These subjects were more prone to develop IGD than reference group (computer only gamers (B = 0.457, odds ratio = 1.579. Smartphone only gamers had the lowest prevalence of IGD, spent the least time and money on gaming, and showed lowest scores of Internet and smartphone addiction. Our findings suggest that gaming device usage patterns may be associated with the occurrence, course, and prognosis of IGD.

32 CFR 516.69 - Introduction.

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2010-07-01

... 32 National Defense 3 2010-07-01 2010-07-01 true Introduction. 516.69 Section 516.69 National Defense Department of Defense (Continued) DEPARTMENT OF THE ARMY AID OF CIVIL AUTHORITIES AND PUBLIC RELATIONS LITIGATION Cooperation With the Office of Special Counsel § 516.69 Introduction. This subpart...

47 CFR 69.109 - Information.

Science.gov (United States)

2010-10-01

... 47 Telecommunication 3 2010-10-01 2010-10-01 false Information. 69.109 Section 69.109... Computation of Charges § 69.109 Information. (a) A charge shall be assessed upon all interexchange carriers..., the projected annual revenue requirement for the Information element shall be divided by 12 to compute...

Feature Usage Explorer: Usage Monitoring and Visualization Tool in HTML5 Based Applications

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Sarunas Marciuska

2013-10-01

Full Text Available Feature Usage Explorer is a JavaScript library, which automatically detects features in HTML5 based applications and monitors their usage. The collected information can be visualized in a Feature Usage Diagram, which is automatically generated from an input json file. Currently, the users of Feature Usage Explorer have to design their own tool in order to generate the json file from collected usage information. This option remains viable when using the library in order not to constraint the user’s choice of preferred data storage. Feature Usage Explorer can be reused in any HTML5 based applications where an understanding of how users interact with the system is required (i.e. user experience and usability studies, human computer interaction field, or requirement prioritization area.

Event-related potentials (ERP and SGIP1 gene polymorphisms in alcoholics: relation to family history of alcoholism and drug usage

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Roman Chwedorowicz

2016-09-01

The present study demonstrated a possible association of target P300 evoked theta and of alcohol dependence with SNPs from the gene SGIP1 in the region of rs10889635, but further studies are required.

Structure of genes and an insertion element in the methane producing archaebacterium Methanobrevibacter smithii.

Science.gov (United States)

Hamilton, P T; Reeve, J N

1985-01-01

DNA fragments cloned from the methanogenic archaebacterium Methanobrevibacter smithii which complement mutations in the purE and proC genes of E. coli have been sequenced. Sequence analyses, transposon mutagenesis and expression in E. coli minicells indicate that purE and proC complementations result from the synthesis of M. smithii polypeptides with molecular weights of 36,697 and 27,836 respectively. The encoding genes appear to be located in operons. The M. smithii genome contains 69% A/T basepairs (bp) which is reflected in unusual codon usages and intergenic regions containing approximately 85% A/T bp. An insertion element, designated ISM1, was found within the cloned M. smithii DNA located adjacent to the proC complementing region. ISM1 is 1381 bp in length, has 29 bp terminal inverted repeat sequences and contains one major ORF encoded in 87% of the ISM1 sequence. ISM1 is mobile, present in approximately 10 copies per genome and integration duplicates 8 bp at the site of insertion. The duplicated sequences show homology with sequences within the 29 bp terminal repeat sequence of ISM1. Comparison of our data with sequences from halophilic archaebacteria suggests that 5'GAANTTTCA and 5'TTTTAATATAAA may be consensus promoter sequences for archaebacteria. These sequences closely resemble the consensus sequences which precede Drosophila heat-shock genes (Pelham 1982; Davidson et al. 1983). Methanogens appear to employ the eubacterial system of mRNA: 16SrRNA hybridization to ensure initiation of translation; the consensus ribosome binding sequence is 5'AGGTGA.

47 CFR 69.309 - Other investment.

Science.gov (United States)

2010-10-01

... 47 Telecommunication 3 2010-10-01 2010-10-01 false Other investment. 69.309 Section 69.309... Apportionment of Net Investment § 69.309 Other investment. Investment that is not apportioned pursuant to §§ 69... category and access elements in the same proportions as the combined investment that is apportioned...

Urinary 1-hydroxypyrene concentrations in Chinese coke oven workers relative to job category, respirator usage, and cigarette smoking

Energy Technology Data Exchange (ETDEWEB)

Bo Chen; Yunping Hu; Lixing Zheng; Qiangyi Wang; Yuanfen Zhou; Taiyi Jin [Fudan University, Shanghai (China). School of Public Health

2007-09-15

1-Hydroxypyrene (1-OHP) is a biomarker of recent exposure to polycyclic aromatic hydrocarbons (PAHs). We investigated whether urinary 1-OHP concentrations in Chinese coke oven workers (COWs) are modulated by job category, respirator usage, and cigarette smoking. The present cross-sectional study measured urinary 1-OHP concentrations in 197 COWs from Coking plant I and 250 COWs from Coking plant II, as well as 220 unexposed referents from Control plant I and 56 referents from Control plant II. Urinary 1-OHP concentrations (geometric mean, {mu}mol/mol creatinine) were 5.18 and 4.21 in workers from Coking plants I and II, respectively. The highest 1-OHP levels in urine were found among topside workers including lidmen, tar chasers, and whistlers. Benchmen had higher 1-OHP levels than other workers at the sideoven. Above 75% of the COWs exceeded the recommended occupational exposure limit of 2.3 {mu}mol/mol creatinine. Respirator usage and increased body mass index (BMI) slightly reduced 1-OHP levels in COWs. Cigarette smoking significantly increased urinary 1-OHP levels in unexposed referents but had no effect in COWs. Chinese COWs, especially topside workers and benchmen, are exposed to high levels of PAHs. Urinary 1-OHP concentrations appear to be modulated by respirator usage and BMI in COWs, as well as by smoking in unexposed referents.

Genome-Wide Analysis of the Synonymous Codon Usage Patterns in Riemerella anatipestifer

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Jibin Liu

2016-08-01

Full Text Available Riemerella anatipestifer (RA belongs to the Flavobacteriaceae family and can cause a septicemia disease in poultry. The synonymous codon usage patterns of bacteria reflect a series of evolutionary changes that enable bacteria to improve tolerance of the various environments. We detailed the codon usage patterns of RA isolates from the available 12 sequenced genomes by multiple codon and statistical analysis. Nucleotide compositions and relative synonymous codon usage (RSCU analysis revealed that A or U ending codons are predominant in RA. Neutrality analysis found no significant correlation between GC12 and GC3 (p > 0.05. Correspondence analysis and ENc-plot results showed that natural selection dominated over mutation in the codon usage bias. The tree of cluster analysis based on RSCU was concordant with dendrogram based on genomic BLAST by neighbor-joining method. By comparative analysis, about 50 highly expressed genes that were orthologs across all 12 strains were found in the top 5% of high CAI value. Based on these CAI values, we infer that RA contains a number of predicted highly expressed coding sequences, involved in transcriptional regulation and metabolism, reflecting their requirement for dealing with diverse environmental conditions. These results provide some useful information on the mechanisms that contribute to codon usage bias and evolution of RA.

Illicit drugs and pharmaceuticals in the environment--forensic applications of environmental data. Part 1: Estimation of the usage of drugs in local communities.

Science.gov (United States)

Kasprzyk-Hordern, Barbara; Dinsdale, Richard M; Guwy, Alan J

2009-06-01

Pharmaceuticals and recently also illicit drugs have been recognised as emerging environmental contaminants due to their potential environmental impact: frequent occurrence, persistence and risk to aquatic life and humans. This manuscript is part one of the two-part study aiming to provide a better understanding and application of environmental data not only for environmental aims but also to meet forensic objectives. An attempt to use wastewater data is made in order to verify patterns of the usage of drugs (in particular illicit) in local communities. The average usage of cocaine in South Wales was estimated at 0.9 g day(-1) 1000 people(-1), which equals 1 tonne of this drug used or disposed of to sewage annually in Wales. The calculated usage of amphetamine denoted 2.5 g day(-1) 1000 people(-1) and is suspected to be an overestimate. Because no analysis of enantiomers of amphetamine was undertaken, no distinction between amphetamine's legal and illicit usage could be made.

Overexpression of antibiotic resistance genes in hospital effluents over time.

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Rowe, Will P M; Baker-Austin, Craig; Verner-Jeffreys, David W; Ryan, Jim J; Micallef, Christianne; Maskell, Duncan J; Pearce, Gareth P

2017-06-01

Effluents contain a diverse abundance of antibiotic resistance genes that augment the resistome of receiving aquatic environments. However, uncertainty remains regarding their temporal persistence, transcription and response to anthropogenic factors, such as antibiotic usage. We present a spatiotemporal study within a river catchment (River Cam, UK) that aims to determine the contribution of antibiotic resistance gene-containing effluents originating from sites of varying antibiotic usage to the receiving environment. Gene abundance in effluents (municipal hospital and dairy farm) was compared against background samples of the receiving aquatic environment (i.e. the catchment source) to determine the resistome contribution of effluents. We used metagenomics and metatranscriptomics to correlate DNA and RNA abundance and identified differentially regulated gene transcripts. We found that mean antibiotic resistance gene and transcript abundances were correlated for both hospital ( ρ  = 0.9, two-tailed P  hospital effluent samples. High β-lactam resistance gene transcript abundance was related to hospital antibiotic usage over time and hospital effluents contained antibiotic residues. We conclude that effluents contribute high levels of antibiotic resistance genes to the aquatic environment; these genes are expressed at significant levels and are possibly related to the level of antibiotic usage at the effluent source. © The Author 2017. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy.

Transcriptome sequencing revealed significant alteration of cortical promoter usage and splicing in schizophrenia.

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Jing Qin Wu

Full Text Available While hybridization based analysis of the cortical transcriptome has provided important insight into the neuropathology of schizophrenia, it represents a restricted view of disease-associated gene activity based on predetermined probes. By contrast, sequencing technology can provide un-biased analysis of transcription at nucleotide resolution. Here we use this approach to investigate schizophrenia-associated cortical gene expression.The data was generated from 76 bp reads of RNA-Seq, aligned to the reference genome and assembled into transcripts for quantification of exons, splice variants and alternative promoters in postmortem superior temporal gyrus (STG/BA22 from 9 male subjects with schizophrenia and 9 matched non-psychiatric controls. Differentially expressed genes were then subjected to further sequence and functional group analysis. The output, amounting to more than 38 Gb of sequence, revealed significant alteration of gene expression including many previously shown to be associated with schizophrenia. Gene ontology enrichment analysis followed by functional map construction identified three functional clusters highly relevant to schizophrenia including neurotransmission related functions, synaptic vesicle trafficking, and neural development. Significantly, more than 2000 genes displayed schizophrenia-associated alternative promoter usage and more than 1000 genes showed differential splicing (FDR<0.05. Both types of transcriptional isoforms were exemplified by reads aligned to the neurodevelopmentally significant doublecortin-like kinase 1 (DCLK1 gene.This study provided the first deep and un-biased analysis of schizophrenia-associated transcriptional diversity within the STG, and revealed variants with important implications for the complex pathophysiology of schizophrenia.

HIV Co-receptor usage in HIV-related non-hodgkin's lymphoma

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Reid Erin

2012-03-01

Full Text Available Abstract In this study 15 banked samples of HIV-related Non-Hodgkin's Lymphoma (NHL cases were tested for HIV co-receptor usage and SDF1 3'A polymorphism. Reportable tropism from 9 plasma samples had 1 (11.1% HIV case with CXCR4 and 8 (88.9% with CCR5 usage, even though most of the cases occurred at a late stage of HIV (2/3 had CD4 counts below 200, where expected CXCR4 usage would be 60%. Based on the expected proportion of less than 50% CCR5 in chronically infected individuals, this would suggest that in NHL may be associated with CCR5 usage (P = 0.04.

Prokaryotic Expression, Purification and Characterization of a Novel Rice Seed Lipoxygenase Gene OsLOX1

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Ren Wang

2008-06-01

Full Text Available Lipoxygenase (LOX, EC1.13.11.12 is a key enzyme during the degradation of lipids in animals and even plants, and also the first key enzyme responsible for the biosynthesis of jasmonate. To purify and characterize the OsLOX1 gene from rice seeds, the entire coding region of the OsLOX1 gene was inserted into an expression vector pET30a(+ and transformed into Escherichia coli BL21 (DE3. Expression of the fusion protein was successfully induced by isopropyl-β-D- thiogalactopyranoside (IPTG and the purified recombinant protein was obtained by His·Bind® Kits. Further assay showed that the purified recombinant protein exhibited the LOX activity. The optimum pH was 4.8 (acetate buffer and the optimum temperature was 30°C for the above enzyme. Thus, the recombinant might confer an available usage for the synthesis of jasmonate in vitro, and also provides a possibility for elucidating the inter-relationship between the primary structure of the plant seed lipoxygenase protein and its physiological functions.

Codon and amino acid usage in two major human pathogens of genus Bartonella--optimization between replicational-transcriptional selection, translational control and cost minimization.

Science.gov (United States)

Das, Sabyasachi; Paul, Sandip; Chatterjee, Sanjib; Dutta, Chitra

2005-01-01

Intra-genomic variation in synonymous codon and amino acid usage in two human pathogens Bartonella henselae and B. quintana has been carried out through multivariate analysis. Asymmetric mutational bias, coupled with replicational-transcriptional selection, has been identified as the prime selection force behind synonymous codon selection--a characteristic of the genus Bartonella, not exhibited by any other alpha-proteobacterial genome. Distinct codon usage patterns and low synonymous divergence values between orthologous sequences of highly expressed genes from the two Bartonella species indicate that there exists a residual intra-strand synonymous codon bias in the highly expressed genes, possibly operating at the level of translation. In the case of amino acid usage, the mean hydropathy level and aromaticity are the major sources of variation, both having nearly equal impact, while strand-specific mutational pressure and gene expressivity strongly influence the inter-strand variations. In both species under study, the highly expressed gene products tend not to contain heavy and/or aromatic residues, following the cost-minimization hypothesis in spite of their intracellular lifestyle. The codon and amino acid usage in these two human pathogens are, therefore, consequences of a complex balance between replicational-transcriptional selection, translational control, protein hydropathy and cost minimization.

Insulin Pump and CGM Usage in the United States and Germany

Science.gov (United States)

Walsh, John; Roberts, Ruth; Weber, Dietmar; Faber-Heinemann, Gabriele; Heinemann, Lutz

2015-01-01

Background: This survey collected and evaluated user responses about routine tasks and preferences regarding insulin pumps and infusion sets (IIS) with comparison of intercountry differences between the United States (US) and Germany (GER), chosen for their large insulin pump populations. Methods: A total of 985 subjects (534 US, 451 GER; 60% female) with type 1 diabetes on pump therapy anonymously answered 20 pump-related questions. US subjects also answered 11 questions about continuous glucose monitoring (CGM) usage. Results: Length of use of insulin cartridges is shorter in US than in GER, mean (SD) 4.3 (5.0) versus 5.3 (3.2) days (P 3 days vs 7.7% for <3 days; P < .01), and with use of an auto-insertion device (vs manual IIS insertion) in the US (7.2% vs 6.9%), but not in GER (7.7% vs 7.9%). Only 47% of pump wearers stated that they were “very satisfied” with their pump (49% US vs 45% GER, ns). However, 98% would recommend the pump to others (95% vs 93%, ns). Analysis of CGM questions showed that 297 (60%) of 496 US responders currently wore one. Of these, 84% said they would recommend CGM to others. CGM wearers who stated they were “very satisfied” with their CGM had lower HbA1c than those who said they were “partly satisfied” (6.9% vs 7.2%). Conclusions: This survey shows interesting differences in real-world use of insulin pumps in 2 large markets, and suggests areas where insulin pumps and CGMs might be improved. PMID:26071425

Usage Record Format Recommendation

CERN Document Server

Nilsen, J.K.; Muller-Pfeerkorn, R

2013-01-01

For resources to be shared, sites must be able to exchange basic accounting and usage data in a common format. This document describes a common format which enables the exchange of basic accounting and usage data from different resources. This record format is intended to facilitate the sharing of usage information, particularly in the area of the accounting of jobs, computing, memory, storage and cloud usage but with a structure that allows an easy extension to other resources. This document describes the Usage Record components both in natural language form and annotated XML. This document does not address how these records should be used, nor does it attempt to dictate the format in which the accounting records are stored. Instead, it denes a common exchange format. Furthermore, nothing is said regarding the communication mechanisms employed to exchange the records, i.e. transport layer, framing, authentication, integrity, etc.

Clonal relationships between thyroid-stimulating hormone receptor-stimulating antibodies illustrate the effect of hypermutation on antibody function

DEFF Research Database (Denmark)

Padoa, Carolyn J; Larsen, Sanne L; Hampe, Christiane S

2009-01-01

relationship and derivation from a single precursor B-cell clone. The IGHV-region genes of the two mAbs underwent high degrees of somatic hypermutation by sharing numerous mutations before diverging, while the IGLV genes evolved separately. Interestingly, the mutations were present in both the complementarity......, in experimentally immunized mice, multiple pathogenic antibodies to TSHR can arise from a single clone by a series of somatic mutations in the V-region genes and may give an insight into how such antibodies develop spontaneously in autoimmune Graves' disease....

Illicit drugs and pharmaceuticals in the environment - Forensic applications of environmental data. Part 1: Estimation of the usage of drugs in local communities

Energy Technology Data Exchange (ETDEWEB)

Kasprzyk-Hordern, Barbara, E-mail: b.kasprzyk-hordern@hud.ac.u [University of Huddersfield, Department of Chemical and Biological Sciences, Queensgate, Huddersfield HD1 3DH (United Kingdom); University of Glamorgan, Sustainable Environment Research Centre, Faculty of Health, Sport and Science, Pontypridd CF37 1DL (United Kingdom); Dinsdale, Richard M.; Guwy, Alan J. [University of Glamorgan, Sustainable Environment Research Centre, Faculty of Health, Sport and Science, Pontypridd CF37 1DL (United Kingdom)

2009-06-15

Pharmaceuticals and recently also illicit drugs have been recognised as emerging environmental contaminants due to their potential environmental impact: frequent occurrence, persistence and risk to aquatic life and humans. This manuscript is part one of the two-part study aiming to provide a better understanding and application of environmental data not only for environmental aims but also to meet forensic objectives. An attempt to use wastewater data is made in order to verify patterns of the usage of drugs (in particular illicit) in local communities. The average usage of cocaine in South Wales was estimated at 0.9 g day{sup -1} 1000 people{sup -1}, which equals 1 tonne of this drug used or disposed of to sewage annually in Wales. The calculated usage of amphetamine denoted 2.5 g day{sup -1} 1000 people{sup -1} and is suspected to be an overestimate. Because no analysis of enantiomers of amphetamine was undertaken, no distinction between amphetamine's legal and illicit usage could be made. - Wastewater as an indicative source of information can be used in forensic applications.

Illicit drugs and pharmaceuticals in the environment - Forensic applications of environmental data. Part 1: Estimation of the usage of drugs in local communities

International Nuclear Information System (INIS)

Kasprzyk-Hordern, Barbara; Dinsdale, Richard M.; Guwy, Alan J.

2009-01-01

Pharmaceuticals and recently also illicit drugs have been recognised as emerging environmental contaminants due to their potential environmental impact: frequent occurrence, persistence and risk to aquatic life and humans. This manuscript is part one of the two-part study aiming to provide a better understanding and application of environmental data not only for environmental aims but also to meet forensic objectives. An attempt to use wastewater data is made in order to verify patterns of the usage of drugs (in particular illicit) in local communities. The average usage of cocaine in South Wales was estimated at 0.9 g day -1 1000 people -1 , which equals 1 tonne of this drug used or disposed of to sewage annually in Wales. The calculated usage of amphetamine denoted 2.5 g day -1 1000 people -1 and is suspected to be an overestimate. Because no analysis of enantiomers of amphetamine was undertaken, no distinction between amphetamine's legal and illicit usage could be made. - Wastewater as an indicative source of information can be used in forensic applications.

A mammalianized synthetic nitroreductase gene for high-level expression

International Nuclear Information System (INIS)

Grohmann, Maik; Paulmann, Nils; Fleischhauer, Sebastian; Vowinckel, Jakob; Priller, Josef; Walther, Diego J

2009-01-01

The nitroreductase/5-(azaridin-1-yl)-2,4-dinitrobenzamide (NTR/CB1954) enzyme/prodrug system is considered as a promising candidate for anti-cancer strategies by gene-directed enzyme prodrug therapy (GDEPT) and has recently entered clinical trials. It requires the genetic modification of tumor cells to express the E. coli enzyme nitroreductase that bioactivates the prodrug CB1954 to a powerful cytotoxin. This metabolite causes apoptotic cell death by DNA interstrand crosslinking. Enhancing the enzymatic NTR activity for CB1954 should improve the therapeutical potential of this enzyme-prodrug combination in cancer gene therapy. We performed de novo synthesis of the bacterial nitroreductase gene adapting codon usage to mammalian preferences. The synthetic gene was investigated for its expression efficacy and ability to sensitize mammalian cells to CB1954 using western blotting analysis and cytotoxicity assays. In our study, we detected cytoplasmic protein aggregates by expressing GFP-tagged NTR in COS-7 cells, suggesting an impaired translation by divergent codon usage between prokaryotes and eukaryotes. Therefore, we generated a synthetic variant of the nitroreductase gene, called ntro, adapted for high-level expression in mammalian cells. A total of 144 silent base substitutions were made within the bacterial ntr gene to change its codon usage to mammalian preferences. The codon-optimized ntro either tagged to gfp or c-myc showed higher expression levels in mammalian cell lines. Furthermore, the ntro rendered several cell lines ten times more sensitive to the prodrug CB1954 and also resulted in an improved bystander effect. Our results show that codon optimization overcomes expression limitations of the bacterial ntr gene in mammalian cells, thereby improving the NTR/CB1954 system at translational level for cancer gene therapy in humans

Usage of Business Simulation Games in Croatia: Perceived Obstacles

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Jovana Zoroja

2013-09-01

Full Text Available Business simulation games (BSGs enhance learning, since they actively involve students in the educational process through game playing. They began to play important role in business education in many universities in Croatia. However, quantitative information on their usage in higher educational institutions (HEIs in Croatia is still scarce. Goals of the paper are to explore: (1 differences among BSGs users and non-users according to demographic characteristics, (2 differences among BSGs users and non-users according to perceived obstacles of BSGs usage, and (3 impact of both demographic characteristics and perceived obstacles on the decision on usage or not-usage of BSGs. A survey was taken in business and economics departments of HEIs in Croatia. A regression model has been used to test the impact of demographic characteristics of educators and the perceived obstacles to the usage of BSGs in educational practice. Results indicate that BSGs usage is currently at a low level, mainly due to the lack of funds and management support. Academic rank, gender, and attitude toward new technologies also impact BSGs usage.

7 CFR 1779.69 - Loan servicing.

Science.gov (United States)

2010-01-01

... 7 Agriculture 12 2010-01-01 2010-01-01 false Loan servicing. 1779.69 Section 1779.69 Agriculture... (CONTINUED) WATER AND WASTE DISPOSAL PROGRAMS GUARANTEED LOANS § 1779.69 Loan servicing. (a) Lender responsibilities. The lender is responsible for servicing the entire loan in accordance with the lender's loan...

33 CFR 159.69 - Motor ratings.

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2010-07-01

... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Motor ratings. 159.69 Section 159.69 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) POLLUTION MARINE SANITATION DEVICES Design, Construction, and Testing § 159.69 Motor ratings. Motors must be rated...

49 CFR 229.69 - Side bearings.

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2010-10-01

... 49 Transportation 4 2010-10-01 2010-10-01 false Side bearings. 229.69 Section 229.69....69 Side bearings. (a) Friction side bearings with springs designed to carry weight may not have more than 25 percent of the springs in any one nest broken. (b) Friction side bearings may not be run in...

Gene Prediction in Metagenomic Fragments with Deep Learning

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Shao-Wu Zhang

2017-01-01

Full Text Available Next generation sequencing technologies used in metagenomics yield numerous sequencing fragments which come from thousands of different species. Accurately identifying genes from metagenomics fragments is one of the most fundamental issues in metagenomics. In this article, by fusing multifeatures (i.e., monocodon usage, monoamino acid usage, ORF length coverage, and Z-curve features and using deep stacking networks learning model, we present a novel method (called Meta-MFDL to predict the metagenomic genes. The results with 10 CV and independent tests show that Meta-MFDL is a powerful tool for identifying genes from metagenomic fragments.

Alternative Promoter Usage in Healthy and Inflamed Tissue

DEFF Research Database (Denmark)

Lilje, Berit

and cell-lines covering the entire human body. This provides a unique dataset to study gene expression, with promoter level precision. Here we use this large collection of data to study alternative transcription start site usage throughout the human body. We find that many alternative transcription start...... with tumour necrosis factor alpha, and on tissue from mice subjected to carbon nanotubes. Both systems show a strong response, with especially alternative transcription start sites being differentially regulated. Taken together this shows that alternative transcription start sites add an important layer...

Association of Proton Pump Inhibitors Usage with Risk of Pneumonia in Dementia Patients.

Science.gov (United States)

Ho, Sai-Wai; Teng, Ying-Hock; Yang, Shun-Fa; Yeh, Han-Wei; Wang, Yu-Hsun; Chou, Ming-Chih; Yeh, Chao-Bin

2017-07-01

To determine the association between usages of proton pump inhibitors (PPIs) and subsequent risk of pneumonia in dementia patients. Retrospective cohort study. Taiwanese National Health Insurance Research Database. The study cohort consisted of 786 dementia patients with new PPI usage and 786 matched dementia patients without PPI usage. The study endpoint was defined as the occurrence of pneumonia. The Cox proportional hazard model was used to estimate the pneumonia risk. Defined daily dose methodology was applied to evaluate the cumulative and dose-response relationships of PPI. Incidence of pneumonia was higher among patients with PPI usage (adjusted hazard ratio (HR) = 1.89; 95% CI = 1.51-2.37). Cox model analysis also demonstrated that age (adjusted HR = 1.05; 95% CI = 1.03-1.06), male gender (adjusted HR = 1.57; 95% CI = 1.25-1.98), underlying cerebrovascular disease (adjusted HR = 1.30; 95% CI = 1.04-1.62), chronic pulmonary disease (adjusted HR = 1.39; 95% CI = 1.09-1.76), congestive heart failure (adjusted HR = 1.54; 95% CI = 1.11-2.13), diabetes mellitus (adjusted HR = 1.54; 95% CI = 1.22-1.95), and usage of antipsychotics (adjusted HR = 1.29; 95% CI = 1.03-1.61) were independent risk factors for pneumonia. However, usage of cholinesterase inhibitors and histamine receptor-2 antagonists were shown to decrease pneumonia risk. PPI usage in dementia patients is associated with an 89% increased risk of pneumonia. © 2017, Copyright the Authors Journal compilation © 2017, The American Geriatrics Society.

10 CFR 36.69 - Irradiation of explosive or flammable materials.

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2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Irradiation of explosive or flammable materials. 36.69... IRRADIATORS Operation of Irradiators § 36.69 Irradiation of explosive or flammable materials. (a) Irradiation... cause radiation overexposures of personnel. (b) Irradiation of more than small quantities of flammable...

Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways.

Science.gov (United States)

Obayashi, Takeshi; Kinoshita, Kengo

2010-05-01

Gene coexpression analyses are a powerful method to predict the function of genes and/or to identify genes that are functionally related to query genes. The basic idea of gene coexpression analyses is that genes with similar functions should have similar expression patterns under many different conditions. This approach is now widely used by many experimental researchers, especially in the field of plant biology. In this review, we will summarize recent successful examples obtained by using our gene coexpression database, ATTED-II. Specifically, the examples will describe the identification of new genes, such as the subunits of a complex protein, the enzymes in a metabolic pathway and transporters. In addition, we will discuss the discovery of a new intercellular signaling factor and new regulatory relationships between transcription factors and their target genes. In ATTED-II, we provide two basic views of gene coexpression, a gene list view and a gene network view, which can be used as guide gene approach and narrow-down approach, respectively. In addition, we will discuss the coexpression effectiveness for various types of gene sets.

Characterization of kappa opioid binding using dynorphin A1-13 and U69,593 in the rat brain

Energy Technology Data Exchange (ETDEWEB)

Devlin, T.; Shoemaker, W.J. (Univ. of Connecticut Health Center, Farmington (USA))

1990-05-01

Previous studies of kappa opioid binding sites have suggested heterogeneous binding to this class of opioid receptors. To further investigate kappa receptor heterogeneity, we analyzed the binding properties of various kappa-selective ligands in rat brain homogenates. Displacement assays were carried out using (3H)bremazocine in the presence of various displacing ligands under mu and delta receptor-blocked conditions. Homologous displacement of (3H)bremazocine produced shallow displacement which best fit a two-site model of drug-receptor interaction. Dynorphin A1-13 and U69,593 exhibited similar biphasic displacement of (3H)bremazocine. Maximal displacement by these ligands, however, represented only approximately 55% of total (3H)bremazocine binding, which suggests the existence of a third component of (3H)bremazocine binding. Biphasic displacement by dynorphin A1-13 was detected in tissue throughout the brain and the spinal cord, whereas the dynorphin-resistant component of (3H)bremazocine binding was uniquely absent in the spinal cord. U50,488H, tifluadom and ethylketocyclazocine appeared to displace from additional, dynorphin-insensitive sites, as their maximal displacement exceeded that seen with either dynorphin A1-13 or U69,593. These results strongly suggest the existence of at least three components of non-mu, non-delta (3H)bremazocine binding in the rat brain: two with differential affinity for dynorphin A1-13 and U69-593 (kappa-1 and kappa-2 sites), and a third (termed here R1) that was further resolved into two binding sites by bremazocine. Preliminary analysis of the R1 component using naloxone revealed one high-affinity site, which may be opiate in nature, and a second site whose binding properties closely resemble those of the sigma receptor described by others.

Generation of a restriction minus enteropathogenic Escherichia coli E2348/69 strain that is efficiently transformed with large, low copy plasmids

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Ward Jordan D

2008-08-01

Full Text Available Abstract Background Many microbes possess restriction-modification systems that protect them from parasitic DNA molecules. Unfortunately, the presence of a restriction-modification system in a given microbe also hampers genetic analysis. Although plasmids can be successfully conjugated into the enteropathogenic Escherichia coli strain E2348/69 and optimized protocols for competent cell preparation have been developed, we found that a large, low copy (~15 bioluminescent reporter plasmid, pJW15, that we modified for use in EPEC, was exceedingly difficult to transform into E2348/69. We reasoned that a restriction-modification system could be responsible for the low transformation efficiency of E2348/69 and sought to identify and inactivate the responsible gene(s, with the goal of creating an easily transformable strain of EPEC that could complement existing protocols for genetic manipulation of this important pathogen. Results Using bioinformatics, we identified genes in the unfinished enteropathogenic Escherichia coli (EPEC strain E2348/69 genome whose predicted products bear homology to the HsdM methyltransferases, HsdS specificity subunits, and HsdR restriction endonucleases of type I restriction-modification systems. We constructed a strain carrying a deletion of the conserved enzymatic domain of the EPEC HsdR homologue, NH4, and showed that its transformation efficiency was up to four orders of magnitude higher than that of the parent strain. Further, the modification capacity of NH4 remained intact, since plasmids that were normally recalcitrant to transformation into E2348/69 could be transformed upon passage through NH4. NH4 was unaffected in virulence factor production, since bundle forming pilus (BFP subunits and type III secreted (T3S proteins were present at equivalent levels to those seen in E2348/69. Further, NH4 was indistinguishable from E2348/69 in tissue culture infection model assays of localized adherence and T3S. Conclusion We

Complementary and Alternative Medicines: Usage and Its Determinant Factors Among Outpatients in Southeast of Iran.

Science.gov (United States)

Ghaedi, Fateme; Dehghan, Mahlagha; Salari, Masoumeh; Sheikhrabori, Akbar

2015-12-13

Prevalence of complementary and alternative medicines is increasing specially in patients with chronic diseases. Therefore, based on the high prevalence of chronic disorders, the present study aimed to determine complementary and alternative medicine usage frequency and its determinant factors. This was a cross-sectional study. Five hundred clients participated in the study by using convenience sampling. A 2-part questionnaire (including demographic form and researcher-created questionnaire) was used for studying the prevalence of using complementary and alternative medicine methods, and users' satisfaction. Findings showed that 75.4% of people used at least one complementary and alternative medicine method. Most of users consumed medicinal plants (69.4%). The most common reason of using a complementary and alternative medicine method was common cold (32.9%). The highest satisfaction belonged to massage (2.94 ± 0.74). The usage of complementary and alternative medicine was 3.22 times higher in people with academic educations when compared with illiterate people. Concerning the high usage of complementary and alternative medicine, it is necessary to train specialists in this field in order to offer such treatments in a safe manner. Also, outcomes of application of complementary and alternative medicine methods should be studied. © The Author(s) 2015.

Women’s Perception, Familial and Mass Media Influence upon Ratus Vaginal Douche Usage in Bali, 2013

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Widyastuti .

2014-08-01

Full Text Available AbstractBackground and purpose: The ratus vaginal douching technique is a treatment by evaporation in the genital area,that compound is called “ratus”. There are a number of controversies surrounding the ratus technique, especiallyregarding the benefits and detrimental aspects. This study applies a behaviour model Green (2007 with a focus onthree factors: the determinant, supporting and stimulant. This study was aimed to understand the relationshipperception, socio economic, familial, and mass media upon ratus vaginal douching usage.Methods: This study used a quantitative approach with an analytic observational cross-sectional design. Study usedrandom sampling of 63 samples that taken from 3 different Spas.Results: The respondents were 44 (69.8% who performed the ratus vaginal douching and 19 (30.2% who had notperformed. Results indicated that the variables of perception, knowledge, familial, and the mass media showed asignificant correlation with the value of (p<0.05. The result of multivariate analysis came from mass media that had thegreatest influence with OR=8.47 (95%CI: 1.21-59.42.Conclusion: Mass media had the greatest influence on the use of the ratus vaginal douching in Bali Province.Keywords: ratus vaginal douching usage, women`s perception, familial, mass media

Prediction of HIV-1 coreceptor usage (tropism) by sequence analysis using a genotypic approach.

Science.gov (United States)

Sierra, Saleta; Kaiser, Rolf; Lübke, Nadine; Thielen, Alexander; Schuelter, Eugen; Heger, Eva; Däumer, Martin; Reuter, Stefan; Esser, Stefan; Fätkenheuer, Gerd; Pfister, Herbert; Oette, Mark; Lengauer, Thomas

2011-12-01

Maraviroc (MVC) is the first licensed antiretroviral drug from the class of coreceptor antagonists. It binds to the host coreceptor CCR5, which is used by the majority of HIV strains in order to infect the human immune cells (Fig. 1). Other HIV isolates use a different coreceptor, the CXCR4. Which receptor is used, is determined in the virus by the Env protein (Fig. 2). Depending on the coreceptor used, the viruses are classified as R5 or X4, respectively. MVC binds to the CCR5 receptor inhibiting the entry of R5 viruses into the target cell. During the course of disease, X4 viruses may emerge and outgrow the R5 viruses. Determination of coreceptor usage (also called tropism) is therefore mandatory prior to administration of MVC, as demanded by EMA and FDA. The studies for MVC efficiency MOTIVATE, MERIT and 1029 have been performed with the Trofile assay from Monogram, San Francisco, U.S.A. This is a high quality assay based on sophisticated recombinant tests. The acceptance for this test for daily routine is rather low outside of the U.S.A., since the European physicians rather tend to work with decentralized expert laboratories, which also provide concomitant resistance testing. These laboratories have undergone several quality assurance evaluations, the last one being presented in 2011. For several years now, we have performed tropism determinations based on sequence analysis from the HIV env-V3 gene region (V3). This region carries enough information to perform a reliable prediction. The genotypic determination of coreceptor usage presents advantages such as: shorter turnover time (equivalent to resistance testing), lower costs, possibility to adapt the results to the patients' needs and possibility of analysing clinical samples with very low or even undetectable viral load (VL), particularly since the number of samples analysed with VL < 1000 copies/μl roughly increased in the last years (Fig. 3). The main steps for tropism testing (Fig. 4) demonstrated in

Dietary fat and risk of colon and rectal cancer with aberrant MLH1 expression, APC or KRAS genes.

Science.gov (United States)

Weijenberg, Matty P; Lüchtenborg, Margreet; de Goeij, Anton F P M; Brink, Mirian; van Muijen, Goos N P; de Bruïne, Adriaan P; Goldbohm, R Alexandra; van den Brandt, Piet A

2007-10-01

To investigate baseline fat intake and the risk of colon and rectal tumors lacking MLH1 (mutL homolog 1, colon cancer, nonpolyposis type 2) repair gene expression and harboring mutations in the APC (adenomatous polyposis coli) tumor suppressor gene and in the KRAS (v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog) oncogene. After 7.3 years of follow-up of the Netherlands Cohort Study (n = 120,852), adjusted incidence rate ratios (RR) and 95% confidence intervals (CI) were computed, based on 401 colon and 130 rectal cancer patients. Total, saturated and monounsaturated fat were not associated with the risk of colon or rectal cancer, or different molecular subgroups. There was also no association between polyunsaturated fat and the risk of overall or subgroups of rectal cancer. Linoleic acid, the most abundant polyunsaturated fatty acid in the diet, was associated with increased risk of colon tumors with only a KRAS mutation and no additional truncating APC mutation or lack of MLH1 expression (RR = 1.41, 95% CI 1.18-1.69 for one standard deviation (i.e., 7.5 g/day) increase in intake, p-trend over the quartiles of intake colon tumors without any of the gene defects, or with tumors harboring aberrations in either MLH1 or APC. Linoleic acid intake is associated with colon tumors with an aberrant KRAS gene, but an intact APC gene and MLH1 expression, suggesting a unique etiology of tumors with specific genetic aberrations.

Isolation and characterisation of cDNA clones representing the genes encoding the major tuber storage protein (dioscorin) of yam (Dioscorea cayenensis Lam.).

Science.gov (United States)

Conlan, R S; Griffiths, L A; Napier, J A; Shewry, P R; Mantell, S; Ainsworth, C

1995-06-01

cDNA clones encoding dioscorins, the major tuber storage proteins (M(r) 32,000) of yam (Dioscorea cayenesis) have been isolated. Two classes of clone (A and B, based on hybrid release translation product sizes and nucleotide sequence differences) which are 84.1% similar in their protein coding regions, were identified. The protein encoded by the open reading frame of the class A cDNA insert is of M(r) 30,015. The difference in observed and calculated molecular mass might be attributed to glycosylation. Nucleotide sequencing and in vitro transcription/translation suggest that the class A dioscorin proteins are synthesised with signal peptides of 18 amino acid residues which are cleaved from the mature peptide. The class A and class B proteins are 69.6% similar with respect to each other, but show no sequence identity with other plant proteins or with the major tuber storage proteins of potato (patatin) or sweet potato (sporamin). Storage protein gene expression was restricted to developing tubers and was not induced by growth conditions known to induce expression of tuber storage protein genes in other plant species. The codon usage of the dioscorin genes suggests that the Dioscoreaceae are more closely related to dicotyledonous than to monocotyledonous plants.

19 CFR 207.69 - Publication of determinations.

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2010-04-01

... 19 Customs Duties 3 2010-04-01 2010-04-01 false Publication of determinations. 207.69 Section 207.69 Customs Duties UNITED STATES INTERNATIONAL TRADE COMMISSION NONADJUDICATIVE INVESTIGATIONS... SUBSIDIZED EXPORTS TO THE UNITED STATES Five-Year Reviews § 207.69 Publication of determinations. Whenever...

Dinucleotide repeat polymorphism in Fms-like tyrosine kinase-1 (Flt-1 gene is not associated with preeclampsia

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Park So-Yeon

2008-07-01

Full Text Available Abstract Background Preeclampsia is a major cause of maternal and perinatal mortality and morbidity. The etiology of preeclampsia remains unclear. Recently, it was shown that misregulation of fms-like tyrosine kinase-1 (Flt-1 in the peripheral blood mononuclear cells of pregnant women results in over-expression of the soluble splice variant of Flt-1, sFlt-1, producing an additional (extra-placental source of sFlt-1 that can contribute to the etiology of preeclampsia. The aim of this study was to investigate the relationship between preeclampsia and a dinucleotide (threonine-glycine; TGn repeat polymorphism in the 3' non-coding region of the Flt-1 gene. Methods The number of the d(TGn repeats was analyzed in 170 patients with preeclampsia and in 202 normotensive pregnancies. The region containing the dinucleotide repeat polymorphism of the Flt-1 gene was amplified by polymerase chain reaction (PCR from the DNA samples and was analyzed by direct PCR sequencing. Results We found 10 alleles of the dinucleotide repeat polymorphism and designated these as allele*12 (A1 through allele*23 (A12 according to the number of the TG repeats, from 12 to 23. The frequency of the 14-repeat allele (A3 was most abundant (63.82% in preeclampsia and 69.06% in controls, followed by the 21-repeat allele (A10; 28.53% in preeclampsia and 23.76% in controls. There was no significant difference in the allele frequency between patients with preeclampsia and normal controls. The most common genotype in preeclamptic and normotensive pregnancies was heterozygous (TG14/(TG21 (41.76% and homozygous (TG14/(TG14 (45.05%, respectively. However, the genotype frequencies were not significantly different between preeclamptic patients and controls. Conclusion This is the first study to characterize the dinucleotide repeat polymorphism of the Flt-1 gene in patients with preeclampsia. We found no differences in the allele or genotype frequencies between patients with preeclampsia and

47 CFR 69.502 - Base factor allocation.

Science.gov (United States)

2010-10-01

... 47 Telecommunication 3 2010-10-01 2010-10-01 false Base factor allocation. 69.502 Section 69.502... Segregation of Common Line Element Revenue Requirement § 69.502 Base factor allocation. Projected revenues from the following shall be deducted from the base factor portion to determine the amount that is...

7 CFR 1767.69 - Index of records.

Science.gov (United States)

2010-01-01

... 7 Agriculture 12 2010-01-01 2010-01-01 false Index of records. 1767.69 Section 1767.69 Agriculture... (CONTINUED) ACCOUNTING REQUIREMENTS FOR RUS ELECTRIC BORROWERS Preservation of Records § 1767.69 Index of records. (a) Each borrower shall maintain a master index of records. The master index shall identify the...

Demographic and health related data of users of a mobile application to support drug adherence is associated with usage duration and intensity.

Directory of Open Access Journals (Sweden)

Stefan Becker

Full Text Available A wealth of mobile applications are designed to support users in their drug intake. When developing software for patients, it is important to understand the differences between individuals who have, who will or who might never adopt mobile interventions. This study analyzes demographic and health-related factors associated with real-life "longer usage" and the "usage-intensity per day" of the mobile application "Medication Plan".Between 2010-2012, the mobile application "Medication Plan" could be downloaded free of charge from the Apple-App-Store. It was aimed at supporting the regular and correct intake of medication. Demographic and health-related data were collected via an online questionnaire. This study analyzed captured data.App-related activities of 1799 users (1708 complete data sets were recorded. 69% (1183/1708 applied "Medication Plan" for more than a day. 74% were male (872/1183, the median age 45 years. Variance analysis showed a significant effect of the users' age with respect to duration of usage (p = 0.025. While the mean duration of use was only 23.3 days for users younger than 21 years, for older users, there was a substantial increase over all age cohorts up to users of 60 years and above (103.9 days. Sex and educational status had no effect. "Daily usage intensity" was directly associated with an increasing number of prescribed medications and increased from an average of 1.87 uses per day and 1 drug per day to on average 3.71 uses per day for users stating to be taking more than 7 different drugs a day (p<0.001. Demographic predictors (sex, age and educational attainment did not affect usage intensity.Users aged 60+ as well as those with complicated therapeutic drug regimens relied on the service we provided for more than three months on average. Mobile applications may be a promising approach to support the treatment of patients with chronic conditions.

Comparison of codon usage bias across Leishmania and Trypanosomatids to understand mRNA secondary structure, relative protein abundance and pathway functions.

Science.gov (United States)

Subramanian, Abhishek; Sarkar, Ram Rup

2015-10-01

Understanding the variations in gene organization and its effect on the phenotype across different Leishmania species, and to study differential clinical manifestations of parasite within the host, we performed large scale analysis of codon usage patterns between Leishmania and other known Trypanosomatid species. We present the causes and consequences of codon usage bias in Leishmania genomes with respect to mutational pressure, translational selection and amino acid composition bias. We establish GC bias at wobble position that governs codon usage bias across Leishmania species, rather than amino acid composition bias. We found that, within Leishmania, homogenous codon context coding for less frequent amino acid pairs and codons avoiding formation of folding structures in mRNA are essentially chosen. We predicted putative differences in global expression between genes belonging to specific pathways across Leishmania. This explains the role of evolution in shaping the otherwise conserved genome to demonstrate species-specific function-level differences for efficient survival. Copyright © 2015 Elsevier Inc. All rights reserved.

Thermal reactor benchmark testing of 69 group library

International Nuclear Information System (INIS)

Liu Guisheng; Wang Yaoqing; Liu Ping; Zhang Baocheng

1994-01-01

Using a code system NSLINK, AMPX master library in WIMS 69 groups structure are made from nuclides relating to 4 newest evaluated nuclear data libraries. Some integrals of 10 thermal reactor benchmark assemblies recommended by the U.S. CSEWG are calculated using rectified PASC-1 code system and compared with foreign results, the authors results are in good agreement with others. 69 group libraries of evaluated data bases in TPFAP interface file are generated with NJOY code system. The k ∞ values of 6 cell lattice assemblies are calculated by the code CBM. The calculated results are analysed and compared

Seatbelt usage: is there an association with obesity?

Science.gov (United States)

Behzad, B; King, D M; Jacobson, S H

2014-09-01

Wearing a seatbelt can prevent motor vehicle crash deaths. While primary seatbelt laws are designed to encourage vehicle passengers to wear seatbelts by allowing law enforcement officers to issue tickets when passengers do not wear seatbelts, discomfort may discourage obese individuals from wearing a seatbelt. The objective of this study is to assess the association between state-level obesity and seatbelt usage rates in the US, and to examine the possible role played by seatbelt laws in these associations. The strength of the association between obesity rates, seatbelt usage, and primary seatbelt laws at the state level is investigated using data from 2006 to 2011. Linear regression analysis is employed. This model estimates that increasing the obesity rate by 1% in a state where a primary seatbelt law (by which law enforcement officers can issue a ticket when seatbelts are not worn) is in effect is associated with a 0.06% decrease in seatbelt usage. However the same percentage of increase in the obesity rate in a state where no primary seatbelt law is in effect is associated with a 0.55% decrease in seatbelt usage. The magnitude of the statistical association between state obesity rates and state-level seatbelt usage is related to the existence of a primary seatbelt law, such that obesity has less impact on seatbelt usage in states where primary seatbelt laws are in effect. Published by Elsevier Ltd.

Fractionated irradiation of H69 small-cell lung cancer cells causes stable radiation and drug resistance with increased MRP1, MRP2, and topoisomerase IIα expression

International Nuclear Information System (INIS)

Henness, Sheridan; Davey, Mary W.; Harvie, Rozelle M.; Davey, Ross A.

2002-01-01

Purpose: After standard treatment with chemotherapy and radiotherapy, small-cell lung cancer (SCLC) often develops resistance to both treatments. Our aims were to establish if fractionated radiation treatment alone would induce radiation and drug resistance in the H69 SCLC cell line, and to determine the mechanisms of resistance. Methods and Materials: H69 SCLC cells were treated with fractionated X-rays to an accumulated dose of 37.5 Gy over 8 months to produce the H69/R38 subline. Drug and radiation resistance was determined using the MTT (3,-4,5 dimethylthiazol-2,5 diphenyltetrazolium bromide) cell viability assay. Protein expression was analyzed by Western blot. Results: The H69/R38 subline was resistant to radiation (2.0 ± 0.2-fold, p<0.0001), cisplatin (14 ± 7-fold, p < 0.001), daunorubicin (6 ± 3-fold, p<0.05), and navelbine (1.7 ± 0.15-fold, p<0.02). This was associated with increased expression of the multidrug resistance-associated proteins, MRP1 and MRP2, and topoisomerase IIα and decreased expression of glutathione-S-transferase π (GSTπ) and bcl-2 and decreased cisplatin accumulation. Treatment with 4 Gy of X-rays produced a 66% decrease in MRP2 in the H69 cells with no change in the H69/R38 cells. This treatment also caused a 5-fold increase in topoisomerase IIα in the H69/R38 cells compared with a 1.5-fold increase in the H69 cells. Conclusions: Fractionated radiation alone can lead to the development of stable radiation and drug resistance and an altered response to radiation in SCLC cells

Relationships of plasma adiponectin level and adiponectin receptors 1 and 2 gene expression to insulin sensitivity and glucose and fat metabolism in monozygotic and dizygotic twins

DEFF Research Database (Denmark)

Storgaard, Heidi; Poulsen, Pernille; Ling, Charlotte

2007-01-01

and muscle AdipoR1/R2 gene expression and the impact of these components on in vivo glucose and fat metabolism. DESIGN AND PARTICIPANTS: Plasma adiponectin and muscle gene expression of AdipoR1/R2 were measured before and during insulin infusion in 89 young and 69 elderly monozygotic and dizygotic twins...... influenced by age, sex, abdominal obesity, and aerobic capacity. Intrapair correlations in monozygotic twins indicated a nongenetic influence of birth weight on plasma adiponectin and AdipoR2 expression. Nonoxidative glucose metabolism was associated with AdipoR1 and plasma adiponectin, in young and elderly...

Pseudouridylation of helix 69 of 23S rRNA is necessary for an effective translation termination

DEFF Research Database (Denmark)

Ejby, Morten; Sørensen, Michael A; Pedersen, Steen

2007-01-01

Escherichia coli strains with inactivated rluD genes were previously found to lack the conserved pseudouridines in helix 69 of 23S ribosomal RNA and to grow slowly. A suppressor mutant was isolated with a near normal growth rate that had changed the conserved Glu-172 codon to a Lys codon in prf...

Designing the optimal robotic milking barn, Part 1: Quantifying facility usage

NARCIS (Netherlands)

Halachmi, I.; Metz, J.H.M.; Maltz, E.; Dijkhuizen, A.A.; Speelman, L.

2000-01-01

The aim of this paper is to explore the stochastic nature of the usage of facilities in a robotic milking barn, independent of the barn layout. It presents experimental data obtained by monitoring 10 dairy cows over a period of 18 days. To minimize restrictions to the access of cows to the

Usage of nuclear data library and proposal to JENDL

International Nuclear Information System (INIS)

Sasaki, M.; Iijima, S.; Kawai, Y.; Matsunobu, H.; Zukeran, A.

1987-01-01

A usage status of nuclear data libraries and proposals to the JENDL library are briefly reviewed. 1) Data bases used in plant design and fuel cycle design fields are summarized. JNDC evaluated data and JENDL are not utilized so much than expected in these fields. 2) Performances between JENDL-2 and ENDF/B-IV are compared in the FBR nuclear design field. JENDL-2 shows good characteristics. 3) Usages of JENDL-2 are shown in the LWR nuclear design field. JENDL-2 isn't always superior to the licensing library. 4) Usages of JENDL-2 are shown in the FBR shielding R D field. JENDL-2 underestimates measured spectra in case of the deep penetration experiment. 5) Based on the above usage status of JENDL-2, proposals to future JENDL and Nuclear Data Center are tabulated. (author)

A Two-Tiered Model for Analyzing Library Web Site Usage Statistics, Part 1: Web Server Logs.

Science.gov (United States)

Cohen, Laura B.

2003-01-01

Proposes a two-tiered model for analyzing web site usage statistics for academic libraries: one tier for library administrators that analyzes measures indicating library use, and a second tier for web site managers that analyzes measures aiding in server maintenance and site design. Discusses the technology of web site usage statistics, and…

Codon-usage-based inhibition of HIV protein synthesis by human schlafen 11.

Science.gov (United States)

Li, Manqing; Kao, Elaine; Gao, Xia; Sandig, Hilary; Limmer, Kirsten; Pavon-Eternod, Mariana; Jones, Thomas E; Landry, Sebastien; Pan, Tao; Weitzman, Matthew D; David, Michael

2012-11-01

In mammals, one of the most pronounced consequences of viral infection is the induction of type I interferons, cytokines with potent antiviral activity. Schlafen (Slfn) genes are a subset of interferon-stimulated early response genes (ISGs) that are also induced directly by pathogens via the interferon regulatory factor 3 (IRF3) pathway. However, many ISGs are of unknown or incompletely understood function. Here we show that human SLFN11 potently and specifically abrogates the production of retroviruses such as human immunodeficiency virus 1 (HIV-1). Our study revealed that SLFN11 has no effect on the early steps of the retroviral infection cycle, including reverse transcription, integration and transcription. Rather, SLFN11 acts at the late stage of virus production by selectively inhibiting the expression of viral proteins in a codon-usage-dependent manner. We further find that SLFN11 binds transfer RNA, and counteracts changes in the tRNA pool elicited by the presence of HIV. Our studies identified a novel antiviral mechanism within the innate immune response, in which SLFN11 selectively inhibits viral protein synthesis in HIV-infected cells by means of codon-bias discrimination.

Epigenetic Alteration by DNA Methylation of ESR1, MYOD1 and hTERT Gene Promoters is Useful for Prediction of Response in Patients of Locally Advanced Invasive Cervical Carcinoma Treated by Chemoradiation.

Science.gov (United States)

Sood, S; Patel, F D; Ghosh, S; Arora, A; Dhaliwal, L K; Srinivasan, R

2015-12-01

Locally advanced invasive cervical cancer [International Federation of Gynecology and Obstetrics (FIGO) IIB/III] is treated by chemoradiation. The response to treatment is variable within a given FIGO stage. Therefore, the aim of the present study was to evaluate the gene promoter methylation profile and corresponding transcript expression of a panel of six genes to identify genes which could predict the response of patients treated by chemoradiation. In total, 100 patients with invasive cervical cancer in FIGO stage IIB/III who underwent chemoradiation treatment were evaluated. Ten patients developed systemic metastases during therapy and were excluded. On the basis of patient follow-up, 69 patients were chemoradiation-sensitive, whereas 21 were chemoradiation-resistant. Gene promoter methylation and gene expression was determined by TaqMan assay and quantitative real-time PCR, respectively, in tissue samples. The methylation frequency of ESR1, BRCA1, RASSF1A, MLH1, MYOD1 and hTERT genes ranged from 40 to 70%. Univariate and hierarchical cluster analysis revealed that gene promoter methylation of MYOD1, ESR1 and hTERT could predict for chemoradiation response. A pattern of unmethylated MYOD1, unmethylated ESR1 and methylated hTERT promoter as well as lower ESR1 transcript levels predicted for chemoradiation resistance. Methylation profiling of a panel of three genes that includes MYOD1, ESR1 and hTERT may be useful to predict the response of invasive cervical carcinoma patients treated with standard chemoradiation therapy. Copyright © 2015 The Royal College of Radiologists. Published by Elsevier Ltd. All rights reserved.

The histone methyltransferase EZH2 as a novel prosurvival factor in clinically aggressive chronic lymphocytic leukemia.

Science.gov (United States)

Papakonstantinou, Nikos; Ntoufa, Stavroula; Chartomatsidou, Elisavet; Kotta, Konstantia; Agathangelidis, Andreas; Giassafaki, Lefki; Karamanli, Tzeni; Bele, Panagiota; Moysiadis, Theodoros; Baliakas, Panagiotis; Sutton, Lesley Ann; Stavroyianni, Niki; Anagnostopoulos, Achilles; Makris, Antonios M; Ghia, Paolo; Rosenquist, Richard; Stamatopoulos, Kostas

2016-06-14

The histone methyltransferase EZH2 induces gene repression through trimethylation of histone H3 at lysine 27 (H3K27me3). EZH2 overexpression has been reported in many types of cancer and associated with poor prognosis. Here we investigated the expression and functionality of EZH2 in chronic lymphocytic leukemia (CLL). Aggressive cases with unmutated IGHV genes (U-CLL) displayed significantly higher EZH2 expression compared to indolent CLL cases with mutated IGHV genes (M-CLL); furthermore, in U-CLL EZH2 expression was upregulated with disease progression. Within U-CLL, EZH2high cases harbored significantly fewer (p = 0.033) TP53 gene abnormalities compared to EZH2low cases. EZH2high cases displayed high H3K27me3 levels and increased viability suggesting that EZH2 is functional and likely confers a survival advantage to CLL cells. This argument was further supported by siRNA-mediated downmodulation of EZH2 which resulted in increased apoptosis. Notably, at the intraclonal level, cell proliferation was significantly associated with EZH2 expression. Treatment of primary CLL cells with EZH2 inhibitors induced downregulation of H3K27me3 levels leading to increased cell apoptosis. In conclusion, EZH2 is overexpressed in adverse-prognosis CLL and associated with increased cell survival and proliferation. Pharmacologic inhibition of EZH2 catalytic activity promotes apoptosis, highlighting EZH2 as a novel potential therapeutic target for specific subgroups of patients with CLL.

METEOR v1.0 - A usage example; METEOR v1.0 - Un ejemplo de uso

Energy Technology Data Exchange (ETDEWEB)

Palomo, E.

1994-07-01

This script describes a detailed example of the use of the software package METEOR for statistical analysis of meteorological data series. A real spanish meteorological data set is chosen to show the capabilities of METEOR. Output files and resultant plots provided of their interpretations are compiled in three appendixes. The original version of METEOR have been developed by Ph. D.Elena Palomo, CIEMAT-IER, GIASE. It is built by linking programs and routines written in FORTRAN 77 and it adds the graphical capabilities of GNUPLOT. The shape of this toolbox was designed following the criteria of modularity, flexibility and agility criteria. All the input, output and analysis options are structured in three main menus: i) the first is aimed to evaluate the quality of the data set; ii) the second is aimed for pre-processing of the data; and iii) the third is aimed towards the statistical analyses and for creating the graphical outputs. Actually the information about METEOR is constituted by three documents written is spanish: 1) METEOR v1.0: User's guide; 2) METEOR v1.0: A usage example; 3) METEOR v1 .0: Design and structure of the software package. (Author)

Side chain requirements for affinity and specificity in D5, an HIV-1 antibody derived from the VH1-69 germline segment.

Science.gov (United States)

Stewart, Alex; Harrison, Joseph S; Regula, Lauren K; Lai, Jonathan R

2013-04-08

Analysis of factors contributing to high affinity antibody-protein interactions provides insight into natural antibody evolution, and guides the design of antibodies with new or enhanced function. We previously studied the interaction between antibody D5 and its target, a designed protein based on HIV-1 gp41 known as 5-Helix, as a model system [Da Silva, G. F.; Harrison, J. S.; Lai, J. R., Biochemistry, 2010, 49, 5464-5472]. Antibody D5 represents an interesting case study because it is derived from the VH1-69 germline segment; this germline segment is characterized by a hydrophobic second heavy chain complementarity determining region (HCDR2) that constitutes the major functional paratope in D5 and several antibodies derived from the same progenitor. Here we explore side chain requirements for affinity and specificity in D5 using phage display. Two D5-based libraries were prepared that contained diversity in all three light chain complementarity determining regions (LCDRs 1-3), and in the third HCDR (HCDR3). The first library allowed residues to vary among a restricted set of six amino acids (Tyr/Ala/Asp/Ser/His/Pro; D5-Lib-I). The second library was designed based on a survey of existing VH1-69 antibody structures (D5-Lib-II). Both libraries were subjected to multiple rounds of selection against 5-Helix, and individual clones characterized. We found that selectants from D5-Lib-I generally had moderate affinity and specificity, while many clones from D5-Lib-II exhibited D5-like properties. Additional analysis of the D5-Lib-II functional population revealed position-specific biases for particular amino acids, many that differed from the identity of those side chains in D5. Together these results suggest that there is some permissiveness for alternative side chains in the LCDRs and HCDR3 of D5, but that replacement with a minimal set of residues is not tolerated in this scaffold for 5-Helix recognition. This work provides novel information about this high

Detection of sodium in the atmosphere of WASP-69b

Science.gov (United States)

Casasayas-Barris, N.; Palle, E.; Nowak, G.; Yan, F.; Nortmann, L.; Murgas, F.

2017-12-01

Context. Transit spectroscopy is one of the most commonly used methods to characterize exoplanets' atmospheres. From the ground, these observations are very challenging due to the terrestrial atmosphere and its intrinsic variations, but high-spectral-resolution observations overcome this difficulty by resolving the spectral lines and taking advantage of the different Doppler velocities of the Earth, the host star, and the exoplanet. Aims: We analyze the transmission spectrum around the Na I doublet at 589 nm of the extrasolar planet WASP-69b, a hot Jupiter orbiting a K-type star with a period of 3.868 days, and compare the analysis to that of the well-known hot Jupiter HD 189733b. We also present the analysis of the Rossiter-McLaughlin (RM) effect for WASP-69b. Methods: We observed two transits of WASP-69b with the High Accuracy Radial velocity Planet Searcher (HARPS-North) spectrograph (R = 115 000) at the Telescopio Nazionale Galileo (TNG). We perform a telluric contamination subtraction based on the comparison between the observed spectra and a telluric water model. Then, the common steps of the differential spectroscopy are followed to extract the transmission spectrum. The method is tested with archival transit data of the extensively studied exoplanet HD 189733b, obtained with the HARPS-South spectrograph at ESO 3.6 m telescope, and then applied to WASP-69b data. Results: For HD 189733b, we spectrally resolve the Na I doublet and measure line contrasts of 0.72 ± 0.05% (D2) and 0.51 ± 0.05% (D1), and full width half maximum (FWHM) values of 0.64 ± 0.04 Å (D2) and 0.60 ± 0.06 Å (D1), in agreement with previously published results. For WASP-69b only the contrast of the D2 line can be measured (5.8 ± 0.3%). This corresponds to a detection at the 5σ-level of excess absorption of 0.5 ± 0.1% in a passband of 1.5 Å. A net blueshift of 0.04 Å is measured for HD 189733b and no shift is obtained for WASP-69b. By measuring the RM effect, we get an angular

Think big--giant genes in bacteria.

Science.gov (United States)

Reva, Oleg; Tümmler, Burkhard

2008-03-01

Long genes should be rare in archaea and eubacteria because of the demanding costs of time and resources for protein production. The search in 580 sequenced prokaryotic genomes, however, revealed 0.2% of all genes to be longer than 5 kb (absolute number: 3732 genes). Eighty giant bacterial genes of more than 20 kb in length were identified in 47 taxa that belong to the phyla Thermotogae (1), Chlorobi (3), Planctomycetes (1), Cyanobacteria (2), Firmicutes (7), Actinobacteria (9), Proteobacteria (23) or Euryarchaeota (1) (number of taxa in brackets). Giant genes are strain-specific, differ in their tetranucleotide usage from the bulk genome and occur preferentially in non-pathogenic environmental bacteria. The two longest bacterial genes known to date were detected in the green sulfur bacterium Chlorobium chlorochromatii CaD3 encoding proteins of 36 806 and 20 647 amino acids, being surpassed in length only by the human titin coding sequence. More than 90% of bacterial giant genes either encode a surface protein or a polyketide/non-ribosomal peptide synthetase. Most surface proteins are acidic, threonine-rich, lack cystein and harbour multiple amino acid repeats. Giant proteins increase bacterial fitness by the production of either weapons towards or shields against animate competitors or hostile environments.

Disparate sequence characteristics of the Erysiphe graminis f.sp. hordei glyceraldehyde-3-phosphate dehydrogenase gene

DEFF Research Database (Denmark)

Christiansen, S.K.; Justesen, A.F.; Giese, H.

1997-01-01

to be similar for all four genes. The results of the codon-usage analysis suggest that Egh is more flexible than other fungi in the choice of nucleotides at the wobble position. Codon-usage preferences in Egh and barley genes indicate a level of difference which may be exploited to discriminate between fungal...

Local Chromatin Features Including PU.1 and IKAROS Binding and H3K4 Methylation Shape the Repertoire of Immunoglobulin Kappa Genes Chosen for V(DJ Recombination

Directory of Open Access Journals (Sweden)

Louise S. Matheson

2017-11-01

Full Text Available V(DJ recombination is essential for the generation of diverse antigen receptor (AgR repertoires. In B cells, immunoglobulin kappa (Igκ light chain recombination follows immunoglobulin heavy chain (Igh recombination. We recently developed the DNA-based VDJ-seq assay for the unbiased quantitation of Igh VH and DH repertoires. Integration of VDJ-seq data with genome-wide datasets revealed that two chromatin states at the recombination signal sequence (RSS of VH genes are highly predictive of recombination in mouse pro-B cells. It is unknown whether local chromatin states contribute to Vκ gene choice during Igκ recombination. Here we adapt VDJ-seq to profile the Igκ VκJκ repertoire and present a comprehensive readout in mouse pre-B cells, revealing highly variable Vκ gene usage. Integration with genome-wide datasets for histone modifications, DNase hypersensitivity, transcription factor binding and germline transcription identified PU.1 binding at the RSS, which was unimportant for Igh, as highly predictive of whether a Vκ gene will recombine or not, suggesting that it plays a binary, all-or-nothing role, priming genes for recombination. Thereafter, the frequency with which these genes recombine was shaped both by the presence and level of enrichment of several other chromatin features, including H3K4 methylation and IKAROS binding. Moreover, in contrast to the Igh locus, the chromatin landscape of the promoter, as well as of the RSS, contributes to Vκ gene recombination. Thus, multiple facets of local chromatin features explain much of the variation in Vκ gene usage. Together, these findings reveal shared and divergent roles for epigenetic features and transcription factors in AgR V(DJ recombination and provide avenues for further investigation of chromatin signatures that may underpin V(DJ-mediated chromosomal translocations.

Gene-based association identifies SPATA13-AS1 as a pharmacogenomic predictor of inhaled short-acting beta-agonist response in multiple population groups.

Science.gov (United States)

Padhukasahasram, B; Yang, J J; Levin, A M; Yang, M; Burchard, E G; Kumar, R; Kwok, P-Y; Seibold, M A; Lanfear, D E; Williams, L K

2014-08-01

Inhaled short-acting beta-agonist (SABA) medication is commonly used in asthma patients to rapidly reverse airway obstruction and improve acute symptoms. We performed a genome-wide association study of SABA medication response using gene-based association tests. A linear mixed model approach was first used for single-nucleotide polymorphism associations, and the results were later combined using GATES to generate gene-based associations. Our results identified SPATA13-AS1 as being significantly associated with SABA bronchodilator response in 328 healthy African Americans. In replication, this gene was associated with SABA response among the two separate groups of African Americans with asthma (n=1073, P=0.011 and n=1968, P=0.014), 149 healthy African Americans (P=0.003) and 556 European Americans with asthma (P=0.041). SPATA13-AS1 was also associated with longitudinal SABA medication usage in the two separate groups of African Americans with asthma (n=658, P=0.047 and n=1968, P=0.025). Future studies are needed to delineate the precise mechanism by which SPATA13-AS1 may influence SABA response.

Cloning of the rat Waf1/Cip1 gene

International Nuclear Information System (INIS)

Belinsky, S.A.; Middleton, S.K.

1994-01-01

The progression of eukaryotic cells through the cell cycle involves the sequential expression of specific genes. This process is regulated by both external and internal stimuli that prevent the cell from prematurely entering the next phase before all macromolecular events have been completed. The activation and subsequent inactivation of cyclin dependent kinases (Cdks) represent one internal stimuli required to regulate the transit of cells from one stage of the cell cycle to the next. Another member of this regulatory cascade is the p53 tumor suppressor gene, which controls a G 1 checkpoint at which the cell cycle can be arrested prior to the initiation of DNA synthesis. Following DNA damage, p53 protein levels rise, and entry into S phase is delayed, presumably to allow time for repair of the lesions. When p53 function is lost, cells containing damaged DNA template enter S phase leading to fixation and propagation of genetic alterations. Recently, evidence linking the growth-suppressing activity of p53 and inactivation of Cdks has been provided by the cloning of the Waf1/Cip1 gene. Waf1/Cip1 encodes a protein of M r 21,000 (p21), which inhibits Cdks in vitro. The overexpression of Waf1/Cip1 in cells inhibits cell growth, suggesting that p21 is a downstream mediator of p53 function. Loss of Waf1/Cip1 gene function could lead to deregulation of the cell cycle and contribute to the development of the neoplastic phenotype in tumors that do not contain mutations in the p53 gene. The purpose of the present investigation was to clone the rat Waf1/Cip1 gene,then determine the frequency for alteration of this gene in lung tumors induced by X-rays

Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance

Directory of Open Access Journals (Sweden)

Zhang Zhang

2012-03-01

Full Text Available Abstract Background Genetic mutation, selective pressure for translational efficiency and accuracy, level of gene expression, and protein function through natural selection are all believed to lead to codon usage bias (CUB. Therefore, informative measurement of CUB is of fundamental importance to making inferences regarding gene function and genome evolution. However, extant measures of CUB have not fully accounted for the quantitative effect of background nucleotide composition and have not statistically evaluated the significance of CUB in sequence analysis. Results Here we propose a novel measure--Codon Deviation Coefficient (CDC--that provides an informative measurement of CUB and its statistical significance without requiring any prior knowledge. Unlike previous measures, CDC estimates CUB by accounting for background nucleotide compositions tailored to codon positions and adopts the bootstrapping to assess the statistical significance of CUB for any given sequence. We evaluate CDC by examining its effectiveness on simulated sequences and empirical data and show that CDC outperforms extant measures by achieving a more informative estimation of CUB and its statistical significance. Conclusions As validated by both simulated and empirical data, CDC provides a highly informative quantification of CUB and its statistical significance, useful for determining comparative magnitudes and patterns of biased codon usage for genes or genomes with diverse sequence compositions.

41 CFR 105-69.105 - Definitions.

Science.gov (United States)

2010-07-01

... services in the private sector. (o) Recipient includes all contractors, subcontractors at any tier, and... 41 Public Contracts and Property Management 3 2010-07-01 2010-07-01 false Definitions. 105-69.105... RESTRICTIONS ON LOBBYING General § 105-69.105 Definitions. For purposes of this part: (a) Agency, as defined in...

Genomic characteristics comparisons of 12 food-related filamentous fungi in tRNA gene set, codon usage and amino acid composition.

Science.gov (United States)

Chen, Wanping; Xie, Ting; Shao, Yanchun; Chen, Fusheng

2012-04-10

Filamentous fungi are widely exploited in food industry due to their abilities to secrete large amounts of enzymes and metabolites. The recent availability of fungal genome sequences has provided an opportunity to explore the genomic characteristics of these food-related filamentous fungi. In this paper, we selected 12 representative filamentous fungi in the areas of food processing and safety, which were Aspergillus clavatus, A. flavus, A. fumigatus, A. nidulans, A. niger, A. oryzae, A. terreus, Monascus ruber, Neurospora crassa, Penicillium chrysogenum, Rhizopus oryzae and Trichoderma reesei, and did the comparative studies of their genomic characteristics of tRNA gene distribution, codon usage pattern and amino acid composition. The results showed that the copy numbers greatly differed among isoaccepting tRNA genes and the distribution seemed to be related with translation process. The results also revealed that genome compositional variation probably constrained the base choice at the third codon, and affected the overall amino acid composition but seemed to have little effect on the integrated physicochemical characteristics of overall amino acids. The further analysis suggested that the wobble pairing and base modification were the important mechanisms in codon-anticodon interaction. In the scope of authors' knowledge, it is the first report about the genomic characteristics analysis of food-related filamentous fungi, which would be informative for the analysis of filamentous fungal genome evolution and their practical application in food industry. Copyright © 2012 Elsevier B.V. All rights reserved.

47 CFR 69.403 - Marketing expense (Account 6610).

Science.gov (United States)

2010-10-01

... 47 Telecommunication 3 2010-10-01 2010-10-01 false Marketing expense (Account 6610). 69.403 Section 69.403 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES (CONTINUED) ACCESS CHARGES Apportionment of Expenses § 69.403 Marketing expense (Account 6610). Marketing...

Appendix 1：Upregulated genes in gene expression profile （P<0.05 ...

Indian Academy of Sciences (India)

lazi

Appendix 1: Upregulated genes in gene expression profile«P2）. Probe_s. Gene_Symbol pvalues foldchange. Probe_S. et_ID. Gene_Symbol pvalues foldchange. et_ID. 1370355. 1393751. Scd1. 1.35E-04. 25.77. Loc1009122508.06E-03. 2.55. -at at. 1398250. 1370870. Acot1. 2.43E-02. 12.18. Me1.

Designation of facility usage categories for Hanford Site facilities

International Nuclear Information System (INIS)

Woodrich, D.D.; Ellingson, D.R.; Scott, M.A.; Schade, A.R.

1991-10-01

This report summarizes the Hanford Site methodology used to ensure facility compliance with the natural phenomena design criteria set forth in the US Department of Energy Orders and guidance. The current Hanford Site methodology for Usage Category designation is based on an engineered feature's safety function and on the feature's assigned Safety Class. At the Hanford Site, Safety Class assignments are deterministic in nature and are based on teh consequences of failure, without regard to the likelihood of occurrence. The report also proposes a risk-based approach to Usage Category designation, which is being considered for future application at the Hanford Site. To establish a proper Usage Category designation, the safety analysis and engineering design processes must be coupled. This union produces a common understanding of the safety function(s) to be accomplished by the design feature(s) and a sound basis for the assignment of Usage Categories to the appropriate systems, structures, and components. 4 refs., 9 figs., 1 tab

Why dentists don't use rubber dam during endodontics and how to promote its usage?

Science.gov (United States)

Madarati, Ahmad A

2016-02-25

This survey study aimed at investigating the frequency of rubber dam use during root canal treatment, identifying influencing factors for not using it by Saudi general dental practitioners (GDPs) and endodontists. It also aimed at identifying measures that increase rubber dam usage. After obtaining an ethical approval, two pilot studies were conducted on staff members at Taibah University College of Dentistry and a group of GDPs. A final online survey was constructed comprising 17 close-ended questions divided into six categories: demographics, endodontic practice, rubber dam use, alternative isolation methods, reasons for not using rubber dam, and measures and policies that increase its usage. The survey was emailed to 375 GDPs randomly selected from the dental register and all endodontists (n = 53) working in the western province, Saudi Arabia. Data were analyzed using the Chi-square and Linear-by-Linear association tests at p ≤ 0.05. The proportion of endodontists who used rubber dam (84.8 %) was significantly greater than that of GDPs (21.6 %) (p < 0.001). Significantly the highest proportion (40.5 %) did not use rubber dam because of unavailability at working place. Most rubber dam none-users (69.25 %) used a combination of other isolation means. The highest proportion of those who used rubber dam were working in the governmental sector (54.3 %). Among rubber dam users, the greatest proportion graduated from Saudi Arabia (57.8 %) compared to those graduated from Egypt (34.3 %) and Syria (22.4 %). There was a significant correlation between the patterns of rubber dam use during undergraduate training and its usage after graduation (p = 0.001). The highest proportion of participants (48.1 %) reported better undergraduate education as the most important factor that would increase rubber dam use in dental practice. Using of rubber dam was not common in Saudi general dental practice. Dentists must follow the recommended standards of care. Place of work and

Local Chromatin Features Including PU.1 and IKAROS Binding and H3K4 Methylation Shape the Repertoire of Immunoglobulin Kappa Genes Chosen for V(D)J Recombination.

Science.gov (United States)

Matheson, Louise S; Bolland, Daniel J; Chovanec, Peter; Krueger, Felix; Andrews, Simon; Koohy, Hashem; Corcoran, Anne E

2017-01-01

V(D)J recombination is essential for the generation of diverse antigen receptor (AgR) repertoires. In B cells, immunoglobulin kappa ( Igκ ) light chain recombination follows immunoglobulin heavy chain ( Igh ) recombination. We recently developed the DNA-based VDJ-seq assay for the unbiased quantitation of Igh VH and DH repertoires. Integration of VDJ-seq data with genome-wide datasets revealed that two chromatin states at the recombination signal sequence (RSS) of VH genes are highly predictive of recombination in mouse pro-B cells. It is unknown whether local chromatin states contribute to Vκ gene choice during Igκ recombination. Here we adapt VDJ-seq to profile the Igκ VκJκ repertoire and present a comprehensive readout in mouse pre-B cells, revealing highly variable Vκ gene usage. Integration with genome-wide datasets for histone modifications, DNase hypersensitivity, transcription factor binding and germline transcription identified PU.1 binding at the RSS, which was unimportant for Igh , as highly predictive of whether a Vκ gene will recombine or not, suggesting that it plays a binary, all-or-nothing role, priming genes for recombination. Thereafter, the frequency with which these genes recombine was shaped both by the presence and level of enrichment of several other chromatin features, including H3K4 methylation and IKAROS binding. Moreover, in contrast to the Igh locus, the chromatin landscape of the promoter, as well as of the RSS, contributes to Vκ gene recombination. Thus, multiple facets of local chromatin features explain much of the variation in Vκ gene usage. Together, these findings reveal shared and divergent roles for epigenetic features and transcription factors in AgR V(D)J recombination and provide avenues for further investigation of chromatin signatures that may underpin V(D)J-mediated chromosomal translocations.

7 CFR 319.69-2 - Freedom from pests.

Science.gov (United States)

2010-01-01

... 7 Agriculture 5 2010-01-01 2010-01-01 false Freedom from pests. 319.69-2 Section 319.69-2 Agriculture Regulations of the Department of Agriculture (Continued) ANIMAL AND PLANT HEALTH INSPECTION... § 319.69-2 Freedom from pests. All packing materials allowed entry under restriction shall be free from...

29 CFR 801.69 - Procedures for initiating review.

Science.gov (United States)

2010-07-01

... 29 Labor 3 2010-07-01 2010-07-01 false Procedures for initiating review. 801.69 Section 801.69 Labor Regulations Relating to Labor (Continued) WAGE AND HOUR DIVISION, DEPARTMENT OF LABOR OTHER LAWS... Vacation of Decision and Order of Administrative Law Judge § 801.69 Procedures for initiating review. (a...

29 CFR 452.69 - Expenses of campaign literature.

Science.gov (United States)

2010-07-01

... 29 Labor 2 2010-07-01 2010-07-01 false Expenses of campaign literature. 452.69 Section 452.69... AND DISCLOSURE ACT OF 1959 Campaign Safeguards § 452.69 Expenses of campaign literature. Each... is no requirement that the union distribute the literature of the candidate free of charge. In the...

GSTM1 Gene Expression Correlates to Leiomyoma Volume Regression in Response to Mifepristone Treatment

Science.gov (United States)

Engman, Mikael; Varghese, Suby; Lagerstedt Robinson, Kristina; Malmgren, Helena; Hammarsjö, Anna; Byström, Birgitta; L Lalitkumar, Parameswaran Grace; Gemzell-Danielsson, Kristina

2013-01-01

Progesterone receptor modulators, such as mifepristone are useful and well tolerated in reducing leiomyoma volume although with large individual variation. The objective of this study was to investigate the molecular basis for the observed leiomyoma volume reduction, in response to mifepristone treatment and explore a possible molecular marker for the selective usage of mifepristone in leiomyoma patients. Premenopausal women (N = 14) were treated with mifepristone 50 mg, every other day for 12 weeks prior to surgery. Women were arbitrarily sub-grouped as good (N = 4), poor (N = 4) responders to treatment or intermediate respondents (N = 3). Total RNA was extracted from leiomyoma tissue, after surgical removal of the tumour and the differential expression of genes were analysed by microarray. The results were analysed using Ingenuity Pathway Analysis software. The glutathione pathway was the most significantly altered canonical pathway in which the glutathione-s transferase mu 1 (GSTM1) gene was significantly over expressed (+8.03 folds) among the good responders compared to non responders. This was further confirmed by Real time PCR (p = 0.024). Correlation of immunoreactive scores (IRS) for GSTM1 accumulation in leiomyoma tissue was seen with base line volume change of leiomyoma R = −0.8 (p = 0.011). Furthermore the accumulation of protein GSTM1 analysed by Western Blot correlated significantly with the percentual leiomyoma volume change R = −0.82 (p = 0.004). Deletion of the GSTM1 gene in leiomyoma biopsies was found in 50% of the mifepristone treated cases, with lower presence of the GSTM1 protein. The findings support a significant role for GSTM1 in leiomyoma volume reduction induced by mifepristone and explain the observed individual variation in this response. Furthermore the finding could be useful to further explore GSTM1 as a biomarker for tailoring medical treatment of uterine leiomyomas for optimizing the response

ICT in University Education: Usage and Challenges among ...

African Journals Online (AJOL)

This study was a survey which explored ICT usage and challenges among academic staff. Thus, the main purpose of this study was to determine the areas of ICT usage among academic staff; identify the obstacles to their ICT usage and identify their areas of training need in ICT usage. Five research questions were posed ...

Influence of certain forces on evolution of synonymous codon usage bias in certain species of three basal orders of aquatic insects.

Science.gov (United States)

Selva Kumar, C; Nair, Rahul R; Sivaramakrishnan, K G; Ganesh, D; Janarthanan, S; Arunachalam, M; Sivaruban, T

2012-12-01

Forces that influence the evolution of synonymous codon usage bias are analyzed in six species of three basal orders of aquatic insects. The rationale behind choosing six species of aquatic insects (three from Ephemeroptera, one from Plecoptera, and two from Odonata) for the present analysis is based on phylogenetic position at the basal clades of the Order Insecta facilitating the understanding of the evolution of codon bias and of factors shaping codon usage patterns in primitive clades of insect lineages and their subtle differences in some of their ecological and environmental requirements in terms of habitat-microhabitat requirements, altitudinal preferences, temperature tolerance ranges, and consequent responses to climate change impacts. The present analysis focuses on open reading frames of the 13 protein-coding genes in the mitochondrial genome of six carefully chosen insect species to get a comprehensive picture of the evolutionary intricacies of codon bias. In all the six species, A and T contents are observed to be significantly higher than G and C, and are used roughly equally. Since transcription hypothesis on codon usage demands A richness and T poorness, it is quite likely that mutation pressure may be the key factor associated with synonymous codon usage (SCU) variations in these species because the mutation hypothesis predicts AT richness and GC poorness in the mitochondrial DNA. Thus, AT-biased mutation pressure seems to be an important factor in framing the SCU variation in all the selected species of aquatic insects, which in turn explains the predominance of A and T ending codons in these species. This study does not find any association between microhabitats and codon usage variations in the mitochondria of selected aquatic insects. However, this study has identified major forces, such as compositional constraints and mutation pressure, which shape patterns of codon usage in mitochondrial genes in the primitive clades of insect lineages.

The Scope of Usage-based Theory

OpenAIRE

Paul eIbbotson

2013-01-01

Usage-based approaches typically draw on a relatively small set of cognitive processes, such as categorization, analogy, and chunking to explain language structure and function. The goal of this paper is to first review the extent to which the “cognitive commitment” of usage-based theory has had success in explaining empirical findings across domains, including language acquisition, processing, and typology. We then look at the overall strengths and weaknesses of usage-based theory and highli...

Dependence of deodorant usage on ABCC11 genotype: scope for personalized genetics in personal hygiene.

Science.gov (United States)

Rodriguez, Santiago; Steer, Colin D; Farrow, Alexandra; Golding, Jean; Day, Ian N M

2013-07-01

Earwax type and axillary odor are genetically determined by rs17822931, a single-nucleotide polymorphism (SNP) located in the ABCC11 gene. The literature has been concerned with the Mendelian trait of earwax, although axillary odor is also Mendelian. Ethnic diversity in rs17822931 exists, with higher frequency of allele A in east Asians. Influence on deodorant usage has not been investigated. In this work, we present a detailed analysis of the rs17822931 effect on deodorant usage in a large (N∼17,000 individuals) population cohort (the Avon Longitudinal Study of Parents and Children (ALSPAC)). We found strong evidence (P=3.7 × 10(-20)) indicating differential deodorant usage according to the rs17822931 genotype. AA homozygotes were almost 5-fold overrepresented in categories of never using deodorant or using it infrequently. However, 77.8% of white European genotypically nonodorous individuals still used deodorant, and 4.7% genotypically odorous individuals did not. We provide evidence of a behavioral effect associated with rs17822931. This effect has a biological basis that can result in a change in the family's environment if an aerosol deodorant is used. It also indicates potential cost saving to the nonodorous and scope for personalized genetics usage in personal hygiene choices, with consequent reduction of inappropriate chemical exposures for some.

Immunoglobulin gene usage in the human anti-pathogen response.

Science.gov (United States)

Newkirk, M M; Rioux, J D

1995-09-01

The human antibody response to foreign pathogens is generated to a relatively small number of target surface proteins and carbohydrates that nonetheless have an extensive array of epitopes. The study of human monoclonal antibodies to different pathogens shows that there are a diversity of mechanisms used to generate a sufficient repertoire of antibodies to combat the invading pathogens. Although many different immunoglobulin gene elements are used to construct the anti-pathogen response, some elements are used more often than would be expected if all elements were used randomly. For example, the immune response to Haemophilus influenzae polysaccharide appears to be quite narrow, being restricted primarily to a specific heavy-chain gene, 3-15, and a lambda light-chain family II member, 4A. In contrast, for the immune response to cytomegalovirus proteins, a wider group of gene elements is needed. It is also surprising that despite an investigator bias for IgG- rather than IgM-secreting immortal B cells (because of their high affinity and neutralizing abilities), 26% of light chains and 13% of heavy chains showed a very low level of somatic mutation, equivalent to an IgM molecule that has not undergone affinity maturation. Although some highly mutated IgG molecules are present in the anti-pathogen response, most of the monoclonal antibodies specific for viruses or bacteria have a level of somatic hypermutation similar to that of the adult IgM repertoire. A number of studies have shown that there are similarities in the antibody responses to pathogens and to self (autoantibodies).(ABSTRACT TRUNCATED AT 250 WORDS)

BS69 : A novel adenovirus E1A-associated protein that inhibits E1A transactivation

NARCIS (Netherlands)

Hateboer, G.; Gennissen, A.M.C.; Ramos, Y.F.M.; Kerkhoven, R.; Sonntag-Buck, V.; Stunnenberg, H.G.; Bernards, R.A.

1995-01-01

The adenovirus ElA gene products are nuclear phosphoproteins that can transactivate the other adenovirus early genes as well as several cellular genes, and can transform primary rodent cells in culture. Transformation and transactivation by ElA proteins is most likely to be mediated through

Collection Usage Pre- and Post-Summon Implementation at the University of Manitoba

Directory of Open Access Journals (Sweden)

Lisa O’Hara

2012-12-01

Full Text Available Objectives – This study examines the use of print and electronic collections bothbefore and after implementation of Summon at the University of Manitoba Libraries.Summon is a web-scale discovery service which allows discovery of all of thematerials the library owns or has access to from a simple search box on the library’sweb page.Methods – COUNTER statistics were used to determine database, e-journal, and ebookstatistics, including database search statistics (DR1 from the COUNTERDatabase Report 1, full-text article downloads from the COUNTER Journal Report 1(JR1, and successful section search requests from the COUNTER Book Report 2 (BR2for electronic resources. Sirsi, the University of Manitoba’s integrated library system,provided statistics on checkouts for the libraries’ circulating print monograph andserial collections. The percentage change from the pre-Summon implementationperiod to the post-Summon implementation period was calculated and these numberswere used to determine whether usage had increased or decreased for both print andelectronic collections.Results – As expected, searches in citation databases decreased because searches wereno longer being carried out in the native database as the metadata from the databaseis included in Summon. E-journal usage increased dramatically and e-book usage alsoincreased for four of six providers examined. Print usage decreased, but the resultswere inconclusive.Conclusions – Summon implementation had a favourable impact on collection usage.

Epithelial-Mesenchymal Transition (EMT) Gene Variants and Epithelial Ovarian Cancer (EOC) Risk.

Science.gov (United States)

Amankwah, Ernest K; Lin, Hui-Yi; Tyrer, Jonathan P; Lawrenson, Kate; Dennis, Joe; Chornokur, Ganna; Aben, Katja K H; Anton-Culver, Hoda; Antonenkova, Natalia; Bruinsma, Fiona; Bandera, Elisa V; Bean, Yukie T; Beckmann, Matthias W; Bisogna, Maria; Bjorge, Line; Bogdanova, Natalia; Brinton, Louise A; Brooks-Wilson, Angela; Bunker, Clareann H; Butzow, Ralf; Campbell, Ian G; Carty, Karen; Chen, Zhihua; Chen, Y Ann; Chang-Claude, Jenny; Cook, Linda S; Cramer, Daniel W; Cunningham, Julie M; Cybulski, Cezary; Dansonka-Mieszkowska, Agnieszka; du Bois, Andreas; Despierre, Evelyn; Dicks, Ed; Doherty, Jennifer A; Dörk, Thilo; Dürst, Matthias; Easton, Douglas F; Eccles, Diana M; Edwards, Robert P; Ekici, Arif B; Fasching, Peter A; Fridley, Brooke L; Gao, Yu-Tang; Gentry-Maharaj, Aleksandra; Giles, Graham G; Glasspool, Rosalind; Goodman, Marc T; Gronwald, Jacek; Harrington, Patricia; Harter, Philipp; Hasmad, Hanis N; Hein, Alexander; Heitz, Florian; Hildebrandt, Michelle A T; Hillemanns, Peter; Hogdall, Claus K; Hogdall, Estrid; Hosono, Satoyo; Iversen, Edwin S; Jakubowska, Anna; Jensen, Allan; Ji, Bu-Tian; Karlan, Beth Y; Jim, Heather; Kellar, Melissa; Kiemeney, Lambertus A; Krakstad, Camilla; Kjaer, Susanne K; Kupryjanczyk, Jolanta; Lambrechts, Diether; Lambrechts, Sandrina; Le, Nhu D; Lee, Alice W; Lele, Shashi; Leminen, Arto; Lester, Jenny; Levine, Douglas A; Liang, Dong; Lim, Boon Kiong; Lissowska, Jolanta; Lu, Karen; Lubinski, Jan; Lundvall, Lene; Massuger, Leon F A G; Matsuo, Keitaro; McGuire, Valerie; McLaughlin, John R; McNeish, Ian; Menon, Usha; Milne, Roger L; Modugno, Francesmary; Moysich, Kirsten B; Ness, Roberta B; Nevanlinna, Heli; Eilber, Ursula; Odunsi, Kunle; Olson, Sara H; Orlow, Irene; Orsulic, Sandra; Weber, Rachel Palmieri; Paul, James; Pearce, Celeste L; Pejovic, Tanja; Pelttari, Liisa M; Permuth-Wey, Jennifer; Pike, Malcolm C; Poole, Elizabeth M; Risch, Harvey A; Rosen, Barry; Rossing, Mary Anne; Rothstein, Joseph H; Rudolph, Anja; Runnebaum, Ingo B; Rzepecka, Iwona K; Salvesen, Helga B; Schernhammer, Eva; Schwaab, Ira; Shu, Xiao-Ou; Shvetsov, Yurii B; Siddiqui, Nadeem; Sieh, Weiva; Song, Honglin; Southey, Melissa C; Spiewankiewicz, Beata; Sucheston-Campbell, Lara; Teo, Soo-Hwang; Terry, Kathryn L; Thompson, Pamela J; Thomsen, Lotte; Tangen, Ingvild L; Tworoger, Shelley S; van Altena, Anne M; Vierkant, Robert A; Vergote, Ignace; Walsh, Christine S; Wang-Gohrke, Shan; Wentzensen, Nicolas; Whittemore, Alice S; Wicklund, Kristine G; Wilkens, Lynne R; Wu, Anna H; Wu, Xifeng; Woo, Yin-Ling; Yang, Hannah; Zheng, Wei; Ziogas, Argyrios; Kelemen, Linda E; Berchuck, Andrew; Schildkraut, Joellen M; Ramus, Susan J; Goode, Ellen L; Monteiro, Alvaro N A; Gayther, Simon A; Narod, Steven A; Pharoah, Paul D P; Sellers, Thomas A; Phelan, Catherine M

2015-12-01

Epithelial-mesenchymal transition (EMT) is a process whereby epithelial cells assume mesenchymal characteristics to facilitate cancer metastasis. However, EMT also contributes to the initiation and development of primary tumors. Prior studies that explored the hypothesis that EMT gene variants contribute to epithelial ovarian carcinoma (EOC) risk have been based on small sample sizes and none have sought replication in an independent population. We screened 15,816 single-nucleotide polymorphisms (SNPs) in 296 genes in a discovery phase using data from a genome-wide association study of EOC among women of European ancestry (1,947 cases and 2,009 controls) and identified 793 variants in 278 EMT-related genes that were nominally (P < 0.05) associated with invasive EOC. These SNPs were then genotyped in a larger study of 14,525 invasive-cancer patients and 23,447 controls. A P-value <0.05 and a false discovery rate (FDR) <0.2 were considered statistically significant. In the larger dataset, GPC6/GPC5 rs17702471 was associated with the endometrioid subtype among Caucasians (odds ratio (OR) = 1.16, 95% CI = 1.07-1.25, P = 0.0003, FDR = 0.19), whereas F8 rs7053448 (OR = 1.69, 95% CI = 1.27-2.24, P = 0.0003, FDR = 0.12), F8 rs7058826 (OR = 1.69, 95% CI = 1.27-2.24, P = 0.0003, FDR = 0.12), and CAPN13 rs1983383 (OR = 0.79, 95% CI = 0.69-0.90, P = 0.0005, FDR = 0.12) were associated with combined invasive EOC among Asians. In silico functional analyses revealed that GPC6/GPC5 rs17702471 coincided with DNA regulatory elements. These results suggest that EMT gene variants do not appear to play a significant role in the susceptibility to EOC. © 2015 WILEY PERIODICALS, INC.

Gene composer: database software for protein construct design, codon engineering, and gene synthesis.

Science.gov (United States)

Lorimer, Don; Raymond, Amy; Walchli, John; Mixon, Mark; Barrow, Adrienne; Wallace, Ellen; Grice, Rena; Burgin, Alex; Stewart, Lance

2009-04-21

To improve efficiency in high throughput protein structure determination, we have developed a database software package, Gene Composer, which facilitates the information-rich design of protein constructs and their codon engineered synthetic gene sequences. With its modular workflow design and numerous graphical user interfaces, Gene Composer enables researchers to perform all common bio-informatics steps used in modern structure guided protein engineering and synthetic gene engineering. An interactive Alignment Viewer allows the researcher to simultaneously visualize sequence conservation in the context of known protein secondary structure, ligand contacts, water contacts, crystal contacts, B-factors, solvent accessible area, residue property type and several other useful property views. The Construct Design Module enables the facile design of novel protein constructs with altered N- and C-termini, internal insertions or deletions, point mutations, and desired affinity tags. The modifications can be combined and permuted into multiple protein constructs, and then virtually cloned in silico into defined expression vectors. The Gene Design Module uses a protein-to-gene algorithm that automates the back-translation of a protein amino acid sequence into a codon engineered nucleic acid gene sequence according to a selected codon usage table with minimal codon usage threshold, defined G:C% content, and desired sequence features achieved through synonymous codon selection that is optimized for the intended expression system. The gene-to-oligo algorithm of the Gene Design Module plans out all of the required overlapping oligonucleotides and mutagenic primers needed to synthesize the desired gene constructs by PCR, and for physically cloning them into selected vectors by the most popular subcloning strategies. We present a complete description of Gene Composer functionality, and an efficient PCR-based synthetic gene assembly procedure with mis-match specific endonuclease

Gene Composer: database software for protein construct design, codon engineering, and gene synthesis

Directory of Open Access Journals (Sweden)

Mixon Mark

2009-04-01

Full Text Available Abstract Background To improve efficiency in high throughput protein structure determination, we have developed a database software package, Gene Composer, which facilitates the information-rich design of protein constructs and their codon engineered synthetic gene sequences. With its modular workflow design and numerous graphical user interfaces, Gene Composer enables researchers to perform all common bio-informatics steps used in modern structure guided protein engineering and synthetic gene engineering. Results An interactive Alignment Viewer allows the researcher to simultaneously visualize sequence conservation in the context of known protein secondary structure, ligand contacts, water contacts, crystal contacts, B-factors, solvent accessible area, residue property type and several other useful property views. The Construct Design Module enables the facile design of novel protein constructs with altered N- and C-termini, internal insertions or deletions, point mutations, and desired affinity tags. The modifications can be combined and permuted into multiple protein constructs, and then virtually cloned in silico into defined expression vectors. The Gene Design Module uses a protein-to-gene algorithm that automates the back-translation of a protein amino acid sequence into a codon engineered nucleic acid gene sequence according to a selected codon usage table with minimal codon usage threshold, defined G:C% content, and desired sequence features achieved through synonymous codon selection that is optimized for the intended expression system. The gene-to-oligo algorithm of the Gene Design Module plans out all of the required overlapping oligonucleotides and mutagenic primers needed to synthesize the desired gene constructs by PCR, and for physically cloning them into selected vectors by the most popular subcloning strategies. Conclusion We present a complete description of Gene Composer functionality, and an efficient PCR-based synthetic gene

Facebook usage by students in higher education

NARCIS (Netherlands)

Wesseling, N.F.; de la Poza, Elena; Dormènech, Jozep; Lloret, Jaime; Vincent Vela, M. Cinta; Zuriaga Agustí, Elena

2015-01-01

In this paper I measure first year student Facebook usage as part of a broader PhD study into the influence of social media usage on the success of students in higher education. A total of 906 students were asked to complete 3 surveys on Facebook usage with their peers, for two consecutive years

Codon Deviation Coefficient: A novel measure for estimating codon usage bias and its statistical significance

KAUST Repository

Zhang, Zhang

2012-03-22

Background: Genetic mutation, selective pressure for translational efficiency and accuracy, level of gene expression, and protein function through natural selection are all believed to lead to codon usage bias (CUB). Therefore, informative measurement of CUB is of fundamental importance to making inferences regarding gene function and genome evolution. However, extant measures of CUB have not fully accounted for the quantitative effect of background nucleotide composition and have not statistically evaluated the significance of CUB in sequence analysis.Results: Here we propose a novel measure--Codon Deviation Coefficient (CDC)--that provides an informative measurement of CUB and its statistical significance without requiring any prior knowledge. Unlike previous measures, CDC estimates CUB by accounting for background nucleotide compositions tailored to codon positions and adopts the bootstrapping to assess the statistical significance of CUB for any given sequence. We evaluate CDC by examining its effectiveness on simulated sequences and empirical data and show that CDC outperforms extant measures by achieving a more informative estimation of CUB and its statistical significance.Conclusions: As validated by both simulated and empirical data, CDC provides a highly informative quantification of CUB and its statistical significance, useful for determining comparative magnitudes and patterns of biased codon usage for genes or genomes with diverse sequence compositions. 2012 Zhang et al; licensee BioMed Central Ltd.

Epithelial-Mesenchymal Transition (EMT) Gene Variants and Epithelial Ovarian Cancer (EOC) Risk

DEFF Research Database (Denmark)

Amankwah, Ernest K.; Lin, Hui-Yi; Tyrer, Jonathan P.

2015-01-01

women of European ancestry (1,947 cases and 2,009 controls) and identified 793 variants in 278 EMT-related genes that were nominally (P ....27-2.24, P = 0.0003, FDR = 0.12), F8 rs7058826 (OR = 1.69, 95% CI = 1.27-2.24, P = 0.0003, FDR = 0.12), and CAPN13 rs1983383 (OR = 0.79, 95% CI = 0.69-0.90, P = 0.0005, FDR = 0.12) were associated with combined invasive EOC among Asians. In silico functional analyses revealed that GPC6/GPC5 rs17702471...

47 CFR 69.123 - Density pricing zones for special access and switched transport.

Science.gov (United States)

2010-10-01

... switched transport. 69.123 Section 69.123 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED... for special access and switched transport. (a)(1) Incumbent local exchange carriers not subject to... at least 15 percent of that carrier's special access and transport revenues within that study area...

Evaluating codon bias perspective in barbiturase gene using ...

African Journals Online (AJOL)

Abdullah

2014-01-08

Jan 8, 2014 ... along with codon usage was done to reveal dynamics of gene evolution and expression ... analysis is a potent approach for detecting mutations, selection methods and finding rationale of biased and unbiased gene changes and hence, evolutionary ... in the perception of the molecular basics plus potential.

36 CFR 7.69 - Ross Lake National Recreation Area.

Science.gov (United States)

2010-07-01

... 36 Parks, Forests, and Public Property 1 2010-07-01 2010-07-01 false Ross Lake National Recreation... INTERIOR SPECIAL REGULATIONS, AREAS OF THE NATIONAL PARK SYSTEM § 7.69 Ross Lake National Recreation Area... snowmobiles the following locations within the Ross Lake National Recreation Area: (1) State Highway 20, that...

Gene-gene interactions of IRF5, STAT4, IKZF1 and ETS1 in systemic lupus erythematosus.

Science.gov (United States)

Dang, J; Shan, S; Li, J; Zhao, H; Xin, Q; Liu, Y; Bian, X; Liu, Q

2014-06-01

Interferon (IFN) activation signaling and T helper 17 (Th17)-cell/B-cell regulation play a critical role in the pathogenesis of systemic lupus erythematosus (SLE). Several studies have provided convincing evidence that polymorphisms in IRF5, STAT4, IKZF1 and ETS1 from these pathways may be involved in SLE by affecting gene expression or epistasis. We analyzed the genetic interaction in known SLE susceptibility loci from the four genes in northern Han Chinese. A total of 946 northern Han Chinese participated in this study (370 unrelated SLE patients and 576 healthy controls). Subjects underwent genotyping for the single-nucleotide polymorphisms (SNPs) rs2004640 in IRF5, rs7574865 in STAT4, rs4917014 in IKZF1 and rs1128334 in ETS1 by use of a TaqMan SNP genotyping assay and direct sequencing. Gene-gene interaction analysis involved direct counting, multifactor dimensionality reduction (MDR) and linear regression analysis. SLE patients and controls differed in allele frequencies of rs7574865, rs1128334 (P < 0.001) and rs4917014 (P < 0.01). Direct counting revealed that the frequency of risk homozygote combinations was higher for SLE patients than controls (P < 0.01). Furthermore, 2-, 3- and 4-way gene-gene epistasis in SLE was confirmed by parametric methods and MDR analysis. Gene expression analysis partially supported the findings. Our study confirmed the association of the IFN pathway or Th17/B-cells and the pathogenesis of SLE, and gene-gene interaction in this pathway may increase the risk of SLE. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

47 CFR 69.125 - Dedicated signalling transport.

Science.gov (United States)

2010-10-01

... 47 Telecommunication 3 2010-10-01 2010-10-01 false Dedicated signalling transport. 69.125 Section... (CONTINUED) ACCESS CHARGES Computation of Charges § 69.125 Dedicated signalling transport. (a) Dedicated signalling transport shall consist of two elements, a signalling link charge and a signalling transfer point...

Targeting the human lysozyme gene on bovine αs1- casein gene ...

African Journals Online (AJOL)

Targeting an exogenous gene into a favorable gene locus and for expression under endogenous regulators is an ideal method in mammary gland bioreactor research. For this purpose, a gene targeting vector was constructed to targeting the human lysozyme gene on bovine αs1-casein gene locus. In this case, the ...

Current usage and future trends in gross digital photography in Canada.

Science.gov (United States)

Horn, Christopher L; DeKoning, Lawrence; Klonowski, Paul; Naugler, Christopher

2014-01-14

The purpose of this study was to assess the current usage, utilization and future direction of digital photography of gross surgical specimens in pathology laboratories across Canada. An online survey consisting of 23 multiple choice and free-text questions regarding gross digital photography was sent out to via email to laboratory staff across Canada involved in gross dissection of surgical specimens. Sixty surveys were returned with representation from most of the provinces. Results showed that gross digital photography is utilized at most institutions (90.0%) and the primary users of the technology are Pathologists (88.0%), Pathologists' Assistants (54.0%) and Pathology residents (50.0%). Most respondents felt that there is a definite need for routine digital imaging of gross surgical specimens in their practice (80.0%). The top two applications for gross digital photography are for documentation of interesting/ complex cases (98.0%) and for teaching purposes (84.0%). The main limitations identified by the survey group are storage space (42.5%) and security issues (40.0%). Respondents indicated that future applications of gross digital photography mostly include teaching (96.6%), presentation at tumour boards/ clinical rounds (89.8%), medico-legal documentation (72.9%) and usage for consultation purposes (69.5%). The results of this survey indicate that pathology staff across Canada currently utilizes gross digital images for regular documentation and educational reasons. They also show that the technology will be needed for future applications in teaching, consultation and medico-legal purposes.

E-book usage: counting the challenges and opportunities

Directory of Open Access Journals (Sweden)

Angela Conyers

2017-07-01

Full Text Available Academic libraries are spending a growing proportion of their increasingly stretched budgets on e-books each year. Within this context, demonstrating a return on investment is imperative, but gathering data about e-resource usage is not always easy.    This article summarizes how libraries and library consortia are acquiring and evaluating e-books, how usage statistics feature within library workflows, the issues faced in doing so and the resulting impact of these issues on understanding usage and informing purchasing of new titles. Discussions with publishers indicate how usage data are being used within the organization, the requirements of customers and the challenges involved in providing usage data for e-books. Assessing and evaluating e-book usage is a complex and challenging task with processes and workflows in development. A transition from print to e-books represents a significant change for libraries, and the availability of reliable usage statistics to support purchase decisions is vital. The article is based on a series of case study interviews with representatives from a small cross-section of academic libraries, library consortia, publishers and aggregators.    This work is of interest to anyone with responsibility for creating, managing, developing, delivering and supporting usage statistics and standards for e-books.

A PRACTICAL ONTOLOGY FOR THE LARGE-SCALE MODELING OF SCHOLARLY ARTIFACTS AND THEIR USAGE

Energy Technology Data Exchange (ETDEWEB)

RODRIGUEZ, MARKO A. [Los Alamos National Laboratory; BOLLEN, JOHAN [Los Alamos National Laboratory; VAN DE SOMPEL, HERBERT [Los Alamos National Laboratory

2007-01-30

The large-scale analysis of scholarly artifact usage is constrained primarily by current practices in usage data archiving, privacy issues concerned with the dissemination of usage data, and the lack of a practical ontology for modeling the usage domain. As a remedy to the third constraint, this article presents a scholarly ontology that was engineered to represent those classes for which large-scale bibliographic and usage data exists, supports usage research, and whose instantiation is scalable to the order of 50 million articles along with their associated artifacts (e.g. authors and journals) and an accompanying 1 billion usage events. The real world instantiation of the presented abstract ontology is a semantic network model of the scholarly community which lends the scholarly process to statistical analysis and computational support. They present the ontology, discuss its instantiation, and provide some example inference rules for calculating various scholarly artifact metrics.

Kinetics of bainite precipitation in the Cu{sub 69.3}Al{sub 18.8}Mn{sub 10.3}Ag{sub 1.6} alloy

Energy Technology Data Exchange (ETDEWEB)

Motta, M.B.J.L. [Departamento de Ciências Exatas e da Terra, UNIFESP, Diadema, SP (Brazil); Adorno, A.T.; Santos, C.M.A. [Departamento de Físico-Química, IQ-UNESP, Araraquara, SP (Brazil); Silva, R.A.G., E-mail: galdino.ricardo@gmail.com [Departamento de Ciências Exatas e da Terra, UNIFESP, Diadema, SP (Brazil)

2017-02-15

In this work the kinetics of bainite precipitation in the Cu{sub 69.3}Al{sub 18.8}Mn{sub 10.3}Ag{sub 1.6} alloy was studied using measurements of microhardness change with aging time, scanning electron microscopy (SEM), energy dispersive X-ray (EDX) analyses, measurements of magnetization change with applied field and high-resolution transmission electron microscopy (HRTEM). The results showed that the bainite precipitation is responsible for the hardness increase in the Cu{sub 69.3}Al{sub 18.8}Mn{sub 10.3}Ag{sub 1.6} alloy. The activation energy value obtained for the bainite precipitation is lower than that found in the literature. This was attributed to the presence of Ag dissolved in matrix and the occurrence of the Cu{sub 3}Al(DO{sub 3}) → Cu{sub 2}AlMn(L2{sub 1}) ordering reaction together with the bainite precipitation. - Highlights: • The activation energy for the bainite precipitation in the Cu{sub 69.3}Al{sub 18.8}Mn{sub 10.3}Ag{sub 1.6} alloy is around 33 kJ/mol. • During bainite precipitation the Cu{sub 2}AlMn phase formation occurs. • The Cu{sub 3}Al(DO{sub 3}) → Cu{sub 2}AlMn(L2{sub 1}) ordering reaction interferes in the activation energy value.

Time-Course Gene Set Analysis for Longitudinal Gene Expression Data.

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Boris P Hejblum

2015-06-01

Full Text Available Gene set analysis methods, which consider predefined groups of genes in the analysis of genomic data, have been successfully applied for analyzing gene expression data in cross-sectional studies. The time-course gene set analysis (TcGSA introduced here is an extension of gene set analysis to longitudinal data. The proposed method relies on random effects modeling with maximum likelihood estimates. It allows to use all available repeated measurements while dealing with unbalanced data due to missing at random (MAR measurements. TcGSA is a hypothesis driven method that identifies a priori defined gene sets with significant expression variations over time, taking into account the potential heterogeneity of expression within gene sets. When biological conditions are compared, the method indicates if the time patterns of gene sets significantly differ according to these conditions. The interest of the method is illustrated by its application to two real life datasets: an HIV therapeutic vaccine trial (DALIA-1 trial, and data from a recent study on influenza and pneumococcal vaccines. In the DALIA-1 trial TcGSA revealed a significant change in gene expression over time within 69 gene sets during vaccination, while a standard univariate individual gene analysis corrected for multiple testing as well as a standard a Gene Set Enrichment Analysis (GSEA for time series both failed to detect any significant pattern change over time. When applied to the second illustrative data set, TcGSA allowed the identification of 4 gene sets finally found to be linked with the influenza vaccine too although they were found to be associated to the pneumococcal vaccine only in previous analyses. In our simulation study TcGSA exhibits good statistical properties, and an increased power compared to other approaches for analyzing time-course expression patterns of gene sets. The method is made available for the community through an R package.

Neurotic Anxiety, Pronoun Usage, and Stress

Science.gov (United States)

Alban, Lewis Sigmund; Groman, William D.

1976-01-01

Attempts to clarify the function of a particular aspect of verbal communication, pronoun usage, by (a) using a Gestalt Therapy theory conceptual framework and (b) experimentally focusing on the relationship of pronoun usage to neurotic anxiety and emotional stress. (Author/RK)

Antisense imaging of epidermal growth factor-induced p21{sup WAF-1/CIP-1} gene expression in MDA-MB-468 human breast cancer xenografts

Energy Technology Data Exchange (ETDEWEB)

Wang, Judy; Chen, Paul; Mrkobrada, Marko [Leslie Dan Faculty of Pharmacy, University of Toronto, 19 Russell Street, M5S 2S2, Toronto, Ontario (Canada); Hu, Meiduo [Leslie Dan Faculty of Pharmacy, University of Toronto, 19 Russell Street, M5S 2S2, Toronto, Ontario (Canada); Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario (Canada); Vallis, Katherine A. [Department of Radiation Oncology, Princess Margaret Hospital, University Health Network, 610 University Avenue, Toronto, Ontario (Canada); Department of Radiation Oncology, University of Toronto, Toronto, Ontario (Canada); Department of Medical Biophysics, University of Toronto, Toronto, Ontario (Canada); Reilly, Raymond M. [Department of Medical Imaging, University of Toronto, Toronto, Ontario (Canada)

2003-09-01

accumulation of {sup 111}In-labeled antisense ODNs in the presence of EGF induction of the p21{sup WAF-1/CIP-1} gene (0.32%{+-}0.06% injected dose/g) compared with normal saline-treated control mice (0.11%{+-}0.07% injected dose/g). The tumor/blood ratio for antisense ODNs in the presence of EGF induction of the p21{sup WAF-1/CIP-1} gene (4.87{+-}0.87) was also significantly higher than for control random sequence ODNs (2.14{+-}0.69) or for mice receiving antisense ODNs but not treated with EGF (2.07{+-}0.37). We conclude that antisense imaging of upregulated p21{sup WAF-1/CIP-1} gene expression is feasible and could represent a promising new molecular imaging strategy for monitoring tumor response in cancer patients. To our knowledge, this study also describes the first report of molecular imaging of the upregulated expression of a downstream gene target of the EGFR, a transmembrane tyrosine kinase receptor. (orig.)

Sequence Alterations of I(Ks Potassium Channel Genes in Kazakhstani Patients with Atrial Fibrillation

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Ainur Akilzhanova

2014-12-01

Full Text Available Introduction. Atrial fibrillation (AF is the most common sustained arrhythmia, and it results in significant morbidity and mortality. However, the pathogenesis of AF remains unclear to date. Recently, more pieces of evidence indicated that AF is a multifactorial disease resulting from the interaction between environmental factors and genetics. Recent studies suggest that genetic mutation of the slow delayed rectifier potassium channel (I(Ks may underlie AF.Objective. To investigate sequence alterations of I(Ks potassium channel genes KCNQ1, KCNE1 and KCNE2 in Kazakhstani patients with atrial fibrillation.Methods. Genomic DNA of 69 cases with atrial fibrillation and 27 relatives were analyzed for mutations in all protein-coding exons and their flanking splice site regions of the genes KCNQ1 (NM_000218.2 and NM_181798.1, KCNE1 (NM_000219.2, and KCNE2 (NM_172201.1 using bidirectional sequencing on the ABI 3730xL DNA Analyzer (Applied Biosystems, Foster City, CA, USA.Results. In total, a disease-causing mutation was identified in 39 of the 69 (56.5% index cases. Of these, altered sequence variants in the KCNQ1 gene accounted for 14.5% of the mutations, whereas a KCNE1 mutation accounted for 43.5% of the mutations and KCNE2 mutation accounted for 1.4% of the mutations. The majority of the distinct mutations were found in a single case (80%, whereas 20% of the mutations were observed more than once. We found two sequence variants in KCNQ1 exon 13 (S546S G1638A and exon 16 (Y662Y, C1986T in ten patients (14.5%. In KCNE1 gene in exon 3 mutation, S59G A280G was observed in 30 of 69 patients (43.5% and KCNE2 exon 2 T10K C29A in 1 patient (1.4%. Genetic cascade screening of 27 relatives to the 69 index cases with an identified mutation revealed 26.9% mutation carriers  who were at risk of cardiac events such as syncope or sudden unexpected death.Conclusion. In this cohort of Kazakhstani index cases with AF, a disease-causing mutation was identified in

Identification of Plagl1/Zac1 binding sites and target genes establishes its role in the regulation of extracellular matrix genes and the imprinted gene network.

Science.gov (United States)

Varrault, Annie; Dantec, Christelle; Le Digarcher, Anne; Chotard, Laëtitia; Bilanges, Benoit; Parrinello, Hugues; Dubois, Emeric; Rialle, Stéphanie; Severac, Dany; Bouschet, Tristan; Journot, Laurent

2017-10-13

PLAGL1/ZAC1 undergoes parental genomic imprinting, is paternally expressed, and is a member of the imprinted gene network (IGN). It encodes a zinc finger transcription factor with anti-proliferative activity and is a candidate tumor suppressor gene on 6q24 whose expression is frequently lost in various neoplasms. Conversely, gain of PLAGL1 function is responsible for transient neonatal diabetes mellitus, a rare genetic disease that results from defective pancreas development. In the present work, we showed that Plagl1 up-regulation was not associated with DNA damage-induced cell cycle arrest. It was rather associated with physiological cell cycle exit that occurred with contact inhibition, growth factor withdrawal, or cell differentiation. To gain insights into Plagl1 mechanism of action, we identified Plagl1 target genes by combining chromatin immunoprecipitation and genome-wide transcriptomics in transfected cell lines. Plagl1-elicited gene regulation correlated with multiple binding to the proximal promoter region through a GC-rich motif. Plagl1 target genes included numerous genes involved in signaling, cell adhesion, and extracellular matrix composition, including collagens. Plagl1 targets also included 22% of the 409 genes that make up the IGN. Altogether, this work identified Plagl1 as a transcription factor that coordinated the regulation of a subset of IGN genes and controlled extracellular matrix composition. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Video personalization for usage environment

Science.gov (United States)

Tseng, Belle L.; Lin, Ching-Yung; Smith, John R.

2002-07-01

A video personalization and summarization system is designed and implemented incorporating usage environment to dynamically generate a personalized video summary. The personalization system adopts the three-tier server-middleware-client architecture in order to select, adapt, and deliver rich media content to the user. The server stores the content sources along with their corresponding MPEG-7 metadata descriptions. Our semantic metadata is provided through the use of the VideoAnnEx MPEG-7 Video Annotation Tool. When the user initiates a request for content, the client communicates the MPEG-21 usage environment description along with the user query to the middleware. The middleware is powered by the personalization engine and the content adaptation engine. Our personalization engine includes the VideoSue Summarization on Usage Environment engine that selects the optimal set of desired contents according to user preferences. Afterwards, the adaptation engine performs the required transformations and compositions of the selected contents for the specific usage environment using our VideoEd Editing and Composition Tool. Finally, two personalization and summarization systems are demonstrated for the IBM Websphere Portal Server and for the pervasive PDA devices.

French grammar and usage

CERN Document Server

Hawkins, Roger

2015-01-01

Long trusted as the most comprehensive, up-to-date and user-friendly grammar available, French Grammar and Usage is a complete guide to French as it is written and spoken today. It includes clear descriptions of all the main grammatical phenomena of French, and their use, illustrated by numerous examples taken from contemporary French, and distinguishes the most common forms of usage, both formal and informal.Key features include:Comprehensive content, covering all the major structures of contemporary French User-friendly organisation offering easy-to-find sections with cross-referencing and i

Factors Influencing Facebook Usage and Facebook Addictive Tendency in University Students: The Role of Online Psychological Privacy and Facebook Usage Motivation.

Science.gov (United States)

Hong, Fu-Yuan; Chiu, Su-Lin

2016-04-01

There are few studies analysing the influence of personal traits and motivation factors on Facebook usage and Facebook addictive tendency as seen in university students. In this study, 225 Taiwanese university students completed a questionnaire to determine their online psychological privacy scale, Facebook usage motivation scale, Facebook usage scale and Facebook addictive tendency scale, in order to evaluate the items that can be conceptualized as the effect of university students' online psychological privacy personal trait and motive factors, and Facebook usage motivation with respect to Facebook usage and Facebook addictive tendency. The study found that a desire for more online psychological privacy correlates with a stronger motivation to use Facebook and more Facebook usage behaviour among university students who may become high-risk groups for Facebook addictive tendency. The study found that a desire for or an acceptance of a lower online psychological privacy correlates with a stronger motivation to use Facebook among university students who may have more Facebook usage behaviour. This study can help understand university students' Facebook usage and Facebook addictive tendency and provide feature indicators for those who may become high-risk groups for Facebook addictive tendency. Finally, this study conducts discussion and proposes relevant suggestions for future study. Copyright © 2014 John Wiley & Sons, Ltd.

14 CFR 158.69 - Recordkeeping and auditing: Collecting carriers.

Science.gov (United States)

2010-01-01

... 14 Aeronautics and Space 3 2010-01-01 2010-01-01 false Recordkeeping and auditing: Collecting carriers. 158.69 Section 158.69 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION, DEPARTMENT OF....69 Recordkeeping and auditing: Collecting carriers. (a) Collecting carriers shall establish and...

49 CFR 393.69 - Liquefied petroleum gas systems.

Science.gov (United States)

2010-10-01

... Protection Association, Battery March Park, Quincy, MA 02269, as follows: (1) A fuel system installed before... ACCESSORIES NECESSARY FOR SAFE OPERATION Fuel Systems § 393.69 Liquefied petroleum gas systems. (a) A fuel system that uses liquefied petroleum gas as a fuel for the operation of a motor vehicle or for the...

Comparison of Nasal Epithelial Smoking-Induced Gene Expression on Affymetrix Exon 1.0 and Gene 1.0 ST Arrays

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Xiaoling Zhang

2013-01-01

Full Text Available We have previously defined the impact of tobacco smoking on nasal epithelium gene expression using Affymetrix Exon 1.0 ST arrays. In this paper, we compared the performance of the Affymetrix GeneChip Human Gene 1.0 ST array with the Human Exon 1.0 ST array for detecting nasal smoking-related gene expression changes. RNA collected from the nasal epithelium of five current smokers and five never smokers was hybridized to both arrays. While the intersample correlation within each array platform was relatively higher in the Gene array than that in the Exon array, the majority of the genes most changed by smoking were tightly correlated between platforms. Although neither array dataset was powered to detect differentially expressed genes (DEGs at a false discovery rate (FDR <0.05, we identified more DEGs than expected by chance using the Gene ST array. These findings suggest that while both platforms show a high degree of correlation for detecting smoking-induced differential gene expression changes, the Gene ST array may be a more cost-effective platform in a clinical setting for gene-level genomewide expression profiling and an effective tool for exploring the host response to cigarette smoking and other inhaled toxins.

Progranulin is a novel independent predictor of disease progression and overall survival in chronic lymphocytic leukemia.

Directory of Open Access Journals (Sweden)

Maria Göbel

Full Text Available Progranulin (Pgrn is a 88 kDa secreted protein with pleiotropic functions including regulation of cell cycle progression, cell motility, wound repair and tumorigenesis. Using microarray based gene expression profiling we have recently demonstrated that the gene for Pgrn, granulin (GRN, is significantly higher expressed in aggressive CD38(+ZAP-70(+ as compared to indolent CD38(-ZAP-70(- chronic lymphocytic leukemia (CLL cases. Here, we measured Pgrn plasma concentrations by enzyme-linked immunosorbent assay (ELISA in the Essen CLL cohort of 131 patients and examined Pgrn for association with established prognostic markers and clinical outcome. We found that high Pgrn plasma levels were strongly associated with adverse risk factors including unmutated IGHV status, expression of CD38 and ZAP-70, poor risk cytogenetics (11q-, 17p- as detected by flourescence in situ hybridization (FISH and high Binet stage. Pgrn as well as the aforementioned risk factors were prognostic for time to first treatment and overall survival in this series. Importantly, these results could be confirmed in the independent multicentric CLL1 cohort of untreated Binet stage A patients (n = 163. Here, multivariate analysis of time to first treatment revealed that high risk Pgrn (HR = 2.06, 95%-CI = 1.13-3.76, p = 0.018, unmutated IGHV status (HR = 5.63, 95%-CI = 3.05-10.38, p<0.001, high risk as defined by the study protocol (HR = 2.06, 95%-CI = 1.09-3.89, p = 0.026 but not poor risk cytogenetics were independent prognostic markers. In summary our results suggest that Pgrn is a novel, robust and independent prognostic marker in CLL that can be easily measured by ELISA.

Progranulin is a novel independent predictor of disease progression and overall survival in chronic lymphocytic leukemia.

Science.gov (United States)

Göbel, Maria; Eisele, Lewin; Möllmann, Michael; Hüttmann, Andreas; Johansson, Patricia; Scholtysik, René; Bergmann, Manuela; Busch, Raymonde; Döhner, Hartmut; Hallek, Michael; Seiler, Till; Stilgenbauer, Stephan; Klein-Hitpass, Ludger; Dührsen, Ulrich; Dürig, Jan

2013-01-01

Progranulin (Pgrn) is a 88 kDa secreted protein with pleiotropic functions including regulation of cell cycle progression, cell motility, wound repair and tumorigenesis. Using microarray based gene expression profiling we have recently demonstrated that the gene for Pgrn, granulin (GRN), is significantly higher expressed in aggressive CD38(+)ZAP-70(+) as compared to indolent CD38(-)ZAP-70(-) chronic lymphocytic leukemia (CLL) cases. Here, we measured Pgrn plasma concentrations by enzyme-linked immunosorbent assay (ELISA) in the Essen CLL cohort of 131 patients and examined Pgrn for association with established prognostic markers and clinical outcome. We found that high Pgrn plasma levels were strongly associated with adverse risk factors including unmutated IGHV status, expression of CD38 and ZAP-70, poor risk cytogenetics (11q-, 17p-) as detected by flourescence in situ hybridization (FISH) and high Binet stage. Pgrn as well as the aforementioned risk factors were prognostic for time to first treatment and overall survival in this series. Importantly, these results could be confirmed in the independent multicentric CLL1 cohort of untreated Binet stage A patients (n = 163). Here, multivariate analysis of time to first treatment revealed that high risk Pgrn (HR = 2.06, 95%-CI = 1.13-3.76, p = 0.018), unmutated IGHV status (HR = 5.63, 95%-CI = 3.05-10.38, p<0.001), high risk as defined by the study protocol (HR = 2.06, 95%-CI = 1.09-3.89, p = 0.026) but not poor risk cytogenetics were independent prognostic markers. In summary our results suggest that Pgrn is a novel, robust and independent prognostic marker in CLL that can be easily measured by ELISA.

Evaluation of a nanotechnology-based approach to induce gene-expression in human THP-1 macrophages under inflammatory conditions.

Science.gov (United States)

Bernal, Laura; Alvarado-Vázquez, Abigail; Ferreira, David Wilson; Paige, Candler A; Ulecia-Morón, Cristina; Hill, Bailey; Caesar, Marina; Romero-Sandoval, E Alfonso

2017-02-01

Macrophages orchestrate the initiation and resolution of inflammation by producing pro- and anti-inflammatory products. An imbalance in these mediators may originate from a deficient or excessive immune response. Therefore, macrophages are valid therapeutic targets to restore homeostasis under inflammatory conditions. We hypothesize that a specific mannosylated nanoparticle effectively induces gene expression in human macrophages under inflammatory conditions without undesirable immunogenic responses. THP-1 macrophages were challenged with lipopolysaccharide (LPS, 5μg/mL). Polyethylenimine (PEI) nanoparticles grafted with a mannose receptor ligand (Man-PEI) were used as a gene delivery method. Nanoparticle toxicity, Man-PEI cellular uptake rate and gene induction efficiency (GFP, CD14 or CD68) were studied. Potential immunogenic responses were evaluated by measuring the production of tumor necrosis factor-alpha (TNF-α), Interleukin (IL)-6 and IL-10. Man-PEI did not produce cytotoxicity, and it was effectively up-taken by THP-1 macrophages (69%). This approach produced a significant expression of GFP (mRNA and protein), CD14 and CD68 (mRNA), and transiently and mildly reduced IL-6 and IL-10 levels in LPS-challenged macrophages. Our results indicate that Man-PEI is suitable for inducing an efficient gene overexpression in human macrophages under inflammatory conditions with limited immunogenic responses. Our promising results set the foundation to test this technology to induce functional anti-inflammatory genes. Copyright © 2016 Elsevier GmbH. All rights reserved.

Ausência de associação entre polimorfismo do gene da interleucina-1 beta e o prognóstico de pacientes com traumatismo crânio-encefálico grave Lack of association between interleukin-1 gene polymorphism and prognosis in severe traumatic brain injury patients

Directory of Open Access Journals (Sweden)

Taís Frederes Krämer Alcalde

2009-12-01

Full Text Available OBJETIVO: O traumatismo crânio-encefálico é a principal causa de óbito em indivíduos com idade entre 1 a 45 anos. O desfecho do traumatismo crânio-encefálico pode estar relacionado, além de fatores pré-morbidade e gravidade do dano, com fatores genéticos. Genes que podem ter relação com o resultado pós-trauma vêm sendo estudados, porém, ainda existem poucas informações sobre a associação entre polimorfismos genéticos e o desfecho do traumatismo crânio-encefálico. O gene da interleucina-1 beta (IL-1B é um dos genes estudados, pois esta citocina encontra-se em níveis elevados após o traumatismo crânio-encefálico e pode afetar de forma negativa seu desfecho. O objetivo do presente estudo foi analisar o polimorfismo -31C/T, localizado na região promotora do gene IL-1B, em pacientes com traumatismo crânio-encefálico grave visando correlacioná-lo com o desfecho primário precoce (alta do centro de terapia intensiva ou morte. MÉTODOS: Foram estudados 69 pacientes internados por traumatismo crânio-encefálico grave em três hospitais de Porto Alegre e região metropolitana. O polimorfismo foi analisado através da reação em cadeia da polimerase, seguida da digestão com enzima de restrição. RESULTADOS: O traumatismo crânio-encefálico grave foi associado a uma mortalidade de 45%. Não foram observadas diferenças significativas nas frequências alélicas e genotípicas entre os grupos de pacientes divididos pelo desfecho do traumatismo crânio-encefálico. CONCLUSÃO: Nossos resultados sugerem que o polimorfismo -31C/T do gene IL-1B não tem impacto significativo no desfecho fatal dos pacientes com traumatismo crânio-encefálico grave.OBJECTIVE: Traumatic brain injury is the major cause of death among individuals between 1-45 years-old. The outcome of traumatic brain injury may be related to brain susceptibility to the injury and genetic factors. Genes that may affect traumatic brain injury outcome are being

Re-Evaluation of Binding Properties of Recombinant Lymphocyte Receptors NKR-P1A and CD69 to Chemically Synthesized Glycans and Peptides

Czech Academy of Sciences Publication Activity Database

Rozbeský, Daniel; Krejzová, Jana; Křenek, Karel; Prchal, J.; Hrabal, R.; Kožíšek, Milan; Weignerová, Lenka; Fiore, M.; Dumy, P.; Renaudet, O.; Křen, Vladimír

2014-01-01

Roč. 15, č. 1 (2014), s. 1271-1283 E-ISSN 1422-0067 R&D Projects: GA MŠk(CZ) LD13042 Institutional support: RVO:61388971 ; RVO:61388963 Keywords : CD69 * NKR-P1A * NMR titration Subject RIV: CE - Biochemistry Impact factor: 2.862, year: 2014

Association analysis of the IL-1 gene cluster polymorphisms with aggressive and chronic periodontitis in the Algerian population.

Science.gov (United States)

Boukortt, Kawther Nourelhouda; Saidi-Ouahrani, Nadjia; Boukerzaza, Boubaker; Ouhaibi-Djellouli, Hadjira; Hachmaoui, Khalida; Benaissa, Fatima Zohra; Taleb, Leila; Drabla-Ouahrani, Hayet; Deba, Tahria; Ouledhamou, Sid Ahmed; Mehtar, Nadhera; Boudjema, Abdellah

2015-10-01

There is strong evidence that genetic as well as environmental factors affect the development of periodontitis. Various studies suggest that genetic polymorphisms of the interleukin-1 (IL-1) genes are associated with an increased risk of developing the pathogenesis. The aim of the present study was to investigate the possible relationship between two polymorphisms of IL-1 gene cluster IL-1B (C+3954T) (rs1143634) and IL-1A (C-889T) (rs1800587) SNPs and the aggressive and chronic periodontitis risk in a case control study in Algerian population. 279 subjects were recruited and received a periodontal examination: 128 healthy controls and 151 cases. From cases, 91 patients were having a chronic disease whereas 60 subjects with aggressive form. All these subjects were genotyped for IL-1A (C-889T) and IL-1B (C+3954T) polymorphisms using TaqMan real time PCR technology. Frequencies of IL-1 alleles, genotypes and the haplotypes were also examined. Significant differences were found in the carriage rate of both minor alleles of the IL-1A (C-889T) and IL-1B (C+3954T) polymorphisms of aggressive periodontitis cases compared with healthy controls (OR [95%CI]=1.61 [1.03-2.49], p=0.03), (OR [95%CI]=1.69 [1.09-2.63], p=0.01), respectively. The result did not reach significance with the chronic form. The studied polymorphisms of the IL-1 genes appear to be associated with susceptibility to aggressive periodontitis (AgP) in the Algerian population. Copyright © 2015 Elsevier Ltd. All rights reserved.

Gamma-gamma angular correlations in the 71 Ga and 69 Ga nuclei

International Nuclear Information System (INIS)

Bairrio Nuevo Junior, A.

1975-01-01

The directional correlations of v-transitions in 71 Ga and 69 Ga have been measured from the decay of 71 Z n and 69 Ge respectively using a Ge(Li)-NaI (f pound) gamma spectrometer. Spin assignments to the levels in Ga at 390(1/2), 487 (5/2 ) , 512(3/2 ) , 964(5/2 ) , 1107(7/2 ) , 1494(9/2*) and 2247 KeV(7/2 ), and 69 Ga at 318(1/2) , 574(5/2) , 872(3/2), 1106(5/2 , 3/2 ) , 1336(7/2 ) , and 1923 KeV(7/2) confirm the results of previous studies on these nuclei . The multipole mixing ratios 6(E2/M1) for several γ-transitions in both nuclei have been determined from the present angular correlation data. The results are: 6(121) - -0.2 * 6(142) * 0.04 - - 0.04, 6(386) = -0.003 - 0.014, 6(487) = 0.04 - 0.07, 5(512) - -0.14 - 0.10, 6(620) = 1.3 * j j and, 6(753) - 0.00 - 0.01 and 6(964) = 0.6 + Q 9 for transitions i n 71 Ga and 6(234) much greater than 0.28 - 0.04 or 0.08 - 0.02, 6(587) - -1.1 - 0.08, 6(1051) much greater than 0.0 - 0.10 and 6(1349) - 0.13 - 0.03 for transitions in 69 Ga . The experimental results are discussed in terms of various nuclear models which are applicable for the odd-A nuclei in this mass region. (author)

Extensive next-generation sequencing analysis in chronic lymphocytic leukemia at diagnosis: clinical and biological correlations

Directory of Open Access Journals (Sweden)

Gian Matteo Rigolin

2016-09-01

Full Text Available Abstract Background In chronic lymphocytic leukemia (CLL, next-generation sequencing (NGS analysis represents a sensitive, reproducible, and resource-efficient technique for routine screening of gene mutations. Methods We performed an extensive biologic characterization of newly diagnosed CLL, including NGS analysis of 20 genes frequently mutated in CLL and karyotype analysis to assess whether NGS and karyotype results could be of clinical relevance in the refinement of prognosis and assessment of risk of progression. The genomic DNA from peripheral blood samples of 200 consecutive CLL patients was analyzed using Ion Torrent Personal Genome Machine, a NGS platform that uses semiconductor sequencing technology. Karyotype analysis was performed using efficient mitogens. Results Mutations were detected in 42.0 % of cases with 42.8 % of mutated patients presenting 2 or more mutations. The presence of mutations by NGS was associated with unmutated IGHV gene (p = 0.009, CD38 positivity (p = 0.010, risk stratification by fluorescence in situ hybridization (FISH (p < 0.001, and the complex karyotype (p = 0.003. A high risk as assessed by FISH analysis was associated with mutations affecting TP53 (p = 0.012, BIRC3 (p = 0.003, and FBXW7 (p = 0.003 while the complex karyotype was significantly associated with TP53, ATM, and MYD88 mutations (p = 0.003, 0.018, and 0.001, respectively. By multivariate analysis, the multi-hit profile (≥2 mutations by NGS was independently associated with a shorter time to first treatment (p = 0.004 along with TP53 disruption (p = 0.040, IGHV unmutated status (p < 0.001, and advanced stage (p < 0.001. Advanced stage (p = 0.010, TP53 disruption (p < 0.001, IGHV unmutated status (p = 0.020, and the complex karyotype (p = 0.007 were independently associated with a shorter overall survival. Conclusions At diagnosis, an extensive biologic characterization including

Computer usage and its relationship with adolescent lifestyle in Hong Kong.

Science.gov (United States)

Ho, S M; Lee, T M

2001-10-01

To determine the patterns of computer usage among adolescents in Hong Kong and to examine whether computer usage is associated with less physical activity and social support among adolescents. A total of 2110 secondary school students (52% boys and 48% girls) in Hong Kong completed a set of questionnaires to measure their computer usage and lifestyle. Mean age of the respondents was 14.16 years (SD = 1.81 years). Computer usage was taped by asking the students to indicate how much time (in minutes) they spent on the computer each day for doing homework assignments; playing computer games; "surfing" the Internet; and communicating with others. The students also provided information on their social-physical lifestyle. Student's t-tests and analysis of variance were used to examine group differences. Pearson product moment correlations were used to explore relationships between computer usage and lifestyle. Boys who use computers for doing homework, "surfing" the Internet, and communicating with others engage in more social-physical activities than others. Boys who use computers to play games tend to be more social-behaviorally inactive. For girls, patterns of computer usage are not related to lifestyle. Computer users tended to engage in social-physical activities more frequently and had higher social support than nonusers. But among computer users, the amount of time spent daily on the computer was not associated with lifestyle. Instead, patterns of computer usage are more related to lifestyle and the relationship is moderated by gender.

MESUR metrics from scholarly usage of resources

CERN Document Server

CERN. Geneva; Van de Sompel, Herbert

2007-01-01

Usage data is increasingly regarded as a valuable resource in the assessment of scholarly communication items. However, the development of quantitative, usage-based indicators of scholarly impact is still in its infancy. The Digital Library Research & Prototyping Team at the Los Alamos National Laboratory's Research library has therefore started a program to expand the set of usage-based tools for the assessment of scholarly communication items. The two-year MESUR project, funded by the Andrew W. Mellon Foundation, aims to define and validate a range of usage-based impact metrics, and issue guidelines with regards to their characteristics and proper application. The MESUR project is constructing a large-scale semantic model of the scholarly community that seamlessly integrates a wide range of bibliographic, citation and usage data. Functioning as a reference data set, this model is analyzed to characterize the intricate networks of typed relationships that exist in the scholarly community. The resulting c...

Empirical study of supervised gene screening

Directory of Open Access Journals (Sweden)

Ma Shuangge

2006-12-01

Full Text Available Abstract Background Microarray studies provide a way of linking variations of phenotypes with their genetic causations. Constructing predictive models using high dimensional microarray measurements usually consists of three steps: (1 unsupervised gene screening; (2 supervised gene screening; and (3 statistical model building. Supervised gene screening based on marginal gene ranking is commonly used to reduce the number of genes in the model building. Various simple statistics, such as t-statistic or signal to noise ratio, have been used to rank genes in the supervised screening. Despite of its extensive usage, statistical study of supervised gene screening remains scarce. Our study is partly motivated by the differences in gene discovery results caused by using different supervised gene screening methods. Results We investigate concordance and reproducibility of supervised gene screening based on eight commonly used marginal statistics. Concordance is assessed by the relative fractions of overlaps between top ranked genes screened using different marginal statistics. We propose a Bootstrap Reproducibility Index, which measures reproducibility of individual genes under the supervised screening. Empirical studies are based on four public microarray data. We consider the cases where the top 20%, 40% and 60% genes are screened. Conclusion From a gene discovery point of view, the effect of supervised gene screening based on different marginal statistics cannot be ignored. Empirical studies show that (1 genes passed different supervised screenings may be considerably different; (2 concordance may vary, depending on the underlying data structure and percentage of selected genes; (3 evaluated with the Bootstrap Reproducibility Index, genes passed supervised screenings are only moderately reproducible; and (4 concordance cannot be improved by supervised screening based on reproducibility.

Systematic study of association of four GABAergic genes: glutamic acid decarboxylase 1 gene, glutamic acid decarboxylase 2 gene, GABA(B) receptor 1 gene and GABA(A) receptor subunit beta2 gene, with schizophrenia using a universal DNA microarray.

Science.gov (United States)

Zhao, Xu; Qin, Shengying; Shi, Yongyong; Zhang, Aiping; Zhang, Jing; Bian, Li; Wan, Chunling; Feng, Guoyin; Gu, Niufan; Zhang, Guangqi; He, Guang; He, Lin

2007-07-01

Several studies have suggested the dysfunction of the GABAergic system as a risk factor in the pathogenesis of schizophrenia. In the present study, case-control association analysis was conducted in four GABAergic genes: two glutamic acid decarboxylase genes (GAD1 and GAD2), a GABA(A) receptor subunit beta2 gene (GABRB2) and a GABA(B) receptor 1 gene (GABBR1). Using a universal DNA microarray procedure we genotyped a total of 20 SNPs on the above four genes in a study involving 292 patients and 286 controls of Chinese descent. Statistically significant differences were observed in the allelic frequencies of the rs187269C/T polymorphism in the GABRB2 gene (P=0.0450, chi(2)=12.40, OR=1.65) and the -292A/C polymorphism in the GAD1 gene (P=0.0450, chi(2)=14.64 OR=1.77). In addition, using an electrophoretic mobility shift assay (EMSA), we discovered differences in the U251 nuclear protein binding to oligonucleotides representing the -292 SNP on the GAD1 gene, which suggests that the -292C allele has reduced transcription factor binding efficiency compared with the 292A allele. Using the multifactor-dimensionality reduction method (MDR), we found that the interactions among the rs187269C/T polymorphism in the GABRB2 gene, the -243A/G polymorphism in the GAD2 gene and the 27379C/T and 661C/T polymorphisms in the GAD1 gene revealed a significant association with schizophrenia (Pschizophrenia in the Chinese population.

Alu Elements as Novel Regulators of Gene Expression in Type 1 Diabetes Susceptibility Genes?

Science.gov (United States)

Kaur, Simranjeet; Pociot, Flemming

2015-07-13

Despite numerous studies implicating Alu repeat elements in various diseases, there is sparse information available with respect to the potential functional and biological roles of the repeat elements in Type 1 diabetes (T1D). Therefore, we performed a genome-wide sequence analysis of T1D candidate genes to identify embedded Alu elements within these genes. We observed significant enrichment of Alu elements within the T1D genes (p-value genes harboring Alus revealed significant enrichment for immune-mediated processes (p-value genes harboring inverted Alus (IRAlus) within their 3' untranslated regions (UTRs) that are known to regulate the expression of host mRNAs by generating double stranded RNA duplexes. Our in silico analysis predicted the formation of duplex structures by IRAlus within the 3'UTRs of T1D genes. We propose that IRAlus might be involved in regulating the expression levels of the host T1D genes.

Construction Of An Optimized Lentiviral Vector Containing Pdx-1 Gene For Transduction Of Stem Cells Towards Gene Therapy Diabetes Type 1

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S Rahmati

2013-02-01

Full Text Available Abstract Background & aim: Nowadays, most of gene therapy protocols are performed by lentiviral vectors. One of the most important factors which is involved in pancreas development and transcription of insulin gene is pancreatic & duodenal homeobox 1 (PDX-1 transcription factor. The goal of this study was to optimize a lentiviral construct, containing pdx-1 gene, to transfect stem cells towards gene therapy of type-1 diabetes. Methods: In this experimental study, first, the pdx-1 gene was multiplied by PCR from pcDNA3.1-pdx-1 and cloned into pTG19-T vector. Then, pdx-1 was subcloned on upstream of IRES-EGFP gene into IRES2-EGFP vector. At the next step, the cloned parts of IRES-EGFP and pdx-1 were isolated and cloned into the lentiviral expression vector pSINTREM in upstream of TRE-CMV gene. After sequencing, final construct was transfected into HEK 293 cells and gene expression of pdx-1 was evaluated using flow cytometry analysis and reverse fluorescent microscopy. Results: Flow cytometry results and inverted fluorescent microscopy observing showed that pdx-1 and GFP genes are expressed in cells transfected with final recombinant construct. Conclusion: Regarding the design of this construct, to ensure long time expression with higher in vivo and in vitro expression efficiency for stem cells and also use of Tet on induced optimized system, it seems that the current construct can be among the best ones to transfect stem cells. Key words: Gene therapy, Diabetes, Stem cells

Perceptions of rural women about contraceptive usage in district Khushab, Punjab.

Science.gov (United States)

Tabassum, Aqeela; Manj, Yasir Nawaz; Gunjial, Tahira Rehman; Nazir, Salma

2016-12-01

To identify the perceptions of rural women about modern contraceptive methods and to ascertain the psycho-social and economic attitude of women about family planning methods. This cross-sectional study was conducted at the University of Sargodha, Sargodha, Pakistan, from December 2014 to March 2015, and comprised married women. The sample was selected using multistage sampling technique through Fitzgibbon table. They were interviewed regarding use of family planning methods. . SPSS 16 was used for data analysis. Of the 500 women, 358(71.6%) were never-users and 142(28.4%) were past-users of family planning methods. Moreover, 52(14.5%) of never-users did not know about a single modern contraceptive method. Of the past-users, 43(30.3%) knew about 1-3 methods and 99(69.7%) about 4 or more methods. Furthermore, 153(30.6%) respondents graded condoms as good, 261(55.2%) agreed that family planning helped in improving one's standard of living to a great extent while 453(90.6%) indicated that family planning methods were not expensive. Besides, 366(71.2%) respondents believed that using contraceptive method caused infertility. Dissatisfaction with methods, method failure, bad experiences with side effects, privacy concerns and different myths associated to the methods were strongly related to the non-usage of modern contraceptive methods.

N-myc downstream-regulated gene 1 promotes oxaliplatin-triggered apoptosis in colorectal cancer cells via enhancing the ubiquitination of Bcl-2.

Science.gov (United States)

Yang, Xiao; Zhu, Fan; Yu, Chaoran; Lu, Jiaoyang; Zhang, Luyang; Lv, Yanfeng; Sun, Jing; Zheng, Minhua

2017-07-18

N-myc downstream-regulated gene1 (NDRG1) has been identified as a potent tumor suppressor gene. The molecular mechanisms of anti-tumor activity of NDRG1 involve its suppressive effects on a variety of tumorigenic signaling pathways. The purpose of this study was to investigate the role of NDRG1 in the apoptosis of colorectal cancer (CRC) cells. We first collected the clinical data of locally advanced rectal cancer (LARC) patients receiving oxaliplatin-based neoadjuvant chemotherapy in our medical center. Correlation analysis revealed that NDRG1 positively associated with the downstaging rates and prognosis of patients. Then, the effects of over-expression and depletion of NDRG1 gene on apoptosis of colorectal cancer were tested in vitro and in vivo. NDRG1 over-expression promoted apoptosis in colorectal cancer cells whereas depletion of NDRG1 resulted in resistance to oxaliplatin treatment. Furthermore, we observed that Bcl-2, a major anti-apoptotic protein, was regulated by NDRG1 at post-transcriptional level. By binding Protein kinase Cα (PKCα), a classical regulating factor of Bcl-2, NDRG1 enhanced the ubiquitination and degradation of Bcl-2, thus promoting apoptosis in CRC cells. In addition, NDRG1 inhibited tumor growth and promoted apoptosis in mouse xenograft model. In conclusion,NDRG1 promotes oxaliplatin-triggered apoptosis in colorectal cancer. Therefore, colorectal cancer patients can be stratified by the expression level of NDRG1. NDRG1-positive patients may benefit from oxaliplatin-containing chemotherapy regimens whereas those with negative NDRG1 expression should avoid the usage of this cytotoxic drug.

Describing Speech Usage in Daily Activities in Typical Adults.

Science.gov (United States)

Anderson, Laine; Baylor, Carolyn R; Eadie, Tanya L; Yorkston, Kathryn M

2016-01-01

"Speech usage" refers to what people want or need to do with their speech to meet communication demands in life roles. The purpose of this study was to contribute to validation of the Levels of Speech Usage scale by providing descriptive data from a sample of adults without communication disorders, comparing this scale to a published Occupational Voice Demands scale and examining predictors of speech usage levels. This is a survey design. Adults aged ≥25 years without reported communication disorders were recruited nationally to complete an online questionnaire. The questionnaire included the Levels of Speech Usage scale, questions about relevant occupational and nonoccupational activities (eg, socializing, hobbies, childcare, and so forth), and demographic information. Participants were also categorized according to Koufman and Isaacson occupational voice demands scale. A total of 276 participants completed the questionnaires. People who worked for pay tended to report higher levels of speech usage than those who do not work for pay. Regression analyses showed employment to be the major contributor to speech usage; however, considerable variance left unaccounted for suggests that determinants of speech usage and the relationship between speech usage, employment, and other life activities are not yet fully defined. The Levels of Speech Usage may be a viable instrument to systematically rate speech usage because it captures both occupational and nonoccupational speech demands. These data from a sample of typical adults may provide a reference to help in interpreting the impact of communication disorders on speech usage patterns. Copyright © 2016 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

Transcriptome Sequencing Revealed Significant Alteration of Cortical Promoter Usage and Splicing in Schizophrenia

Science.gov (United States)

Wu, Jing Qin; Wang, Xi; Beveridge, Natalie J.; Tooney, Paul A.; Scott, Rodney J.; Carr, Vaughan J.; Cairns, Murray J.

2012-01-01

Background While hybridization based analysis of the cortical transcriptome has provided important insight into the neuropathology of schizophrenia, it represents a restricted view of disease-associated gene activity based on predetermined probes. By contrast, sequencing technology can provide un-biased analysis of transcription at nucleotide resolution. Here we use this approach to investigate schizophrenia-associated cortical gene expression. Methodology/Principal Findings The data was generated from 76 bp reads of RNA-Seq, aligned to the reference genome and assembled into transcripts for quantification of exons, splice variants and alternative promoters in postmortem superior temporal gyrus (STG/BA22) from 9 male subjects with schizophrenia and 9 matched non-psychiatric controls. Differentially expressed genes were then subjected to further sequence and functional group analysis. The output, amounting to more than 38 Gb of sequence, revealed significant alteration of gene expression including many previously shown to be associated with schizophrenia. Gene ontology enrichment analysis followed by functional map construction identified three functional clusters highly relevant to schizophrenia including neurotransmission related functions, synaptic vesicle trafficking, and neural development. Significantly, more than 2000 genes displayed schizophrenia-associated alternative promoter usage and more than 1000 genes showed differential splicing (FDRschizophrenia-associated transcriptional diversity within the STG, and revealed variants with important implications for the complex pathophysiology of schizophrenia. PMID:22558445

41 CFR 105-69.205 - Professional and technical services.

Science.gov (United States)

2010-07-01

... any professional or technical discipline. For example, drafting of a legal document accompanying a bid... technical services. 105-69.205 Section 105-69.205 Public Contracts and Property Management Federal Property... technical services. (a) The prohibition on the use of appropriated funds, in § 105-69.100 (a), does not...

41 CFR 105-69.300 - Professional and technical services.

Science.gov (United States)

2010-07-01

... or technical discipline. For example, drafting or a legal document accompanying a bid or proposal by... technical services. 105-69.300 Section 105-69.300 Public Contracts and Property Management Federal Property... and technical services. (a) The prohibition on the use of appropriated funds, in § 105-69.100 (a...

World Wide Web Usage Mining Systems and Technologies

Directory of Open Access Journals (Sweden)

Wen-Chen Hu

2003-08-01

Full Text Available Web usage mining is used to discover interesting user navigation patterns and can be applied to many real-world problems, such as improving Web sites/pages, making additional topic or product recommendations, user/customer behavior studies, etc. This article provides a survey and analysis of current Web usage mining systems and technologies. A Web usage mining system performs five major tasks: i data gathering, ii data preparation, iii navigation pattern discovery, iv pattern analysis and visualization, and v pattern applications. Each task is explained in detail and its related technologies are introduced. A list of major research systems and projects concerning Web usage mining is also presented, and a summary of Web usage mining is given in the last section.

Determination of Coreceptor Usage of Human Immunodeficiency Virus Type 1 from Patient Plasma Samples by Using a Recombinant Phenotypic Assay

Science.gov (United States)

Trouplin, Virginie; Salvatori, Francesca; Cappello, Fanny; Obry, Veronique; Brelot, Anne; Heveker, Nikolaus; Alizon, Marc; Scarlatti, Gabriella; Clavel, François; Mammano, Fabrizio

2001-01-01

We developed a recombinant virus technique to determine the coreceptor usage of human immunodeficiency virus type 1 (HIV-1) from plasma samples, the source expected to represent the most actively replicating virus population in infected subjects. This method is not subject to selective bias associated with virus isolation in culture, a step required for conventional tropism determination procedures. The addition of a simple subcloning step allowed semiquantitative evaluation of virus populations with a different coreceptor (CCR5 or CXCR4) usage specificity present in each plasma sample. This procedure detected mixtures of CCR5- and CXCR4-exclusive virus populations as well as dualtropic viral variants, in variable proportions. Sequence analysis of dualtropic clones indicated that changes in the V3 loop are necessary for the use of CXCR4 as a coreceptor, but the overall context of the V1-V3 region is important to preserve the capacity to use CCR5. This convenient technique can greatly assist the study of virus evolution and compartmentalization in infected individuals. PMID:11119595

19 CFR 10.69 - Samples to Great Britain and Ireland under reciprocal agreement.

Science.gov (United States)

2010-04-01

... the United States and one for the use of the foreign customs authorities. The latter copy must have... 19 Customs Duties 1 2010-04-01 2010-04-01 false Samples to Great Britain and Ireland under reciprocal agreement. 10.69 Section 10.69 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF...

The -160 (C>A) CDH1 Gene Promoter Polymorphism and Its Relationship with Survival of Patients with Gastric Cancer in

Science.gov (United States)

Menbari, Mohammad Nazir; Nasseri, Sherko; Menbari, Neda; Mehdiabadi, Ramin; Alipur, Yousef; Roshani, Daem

2017-06-25

Introduction: Gastric cancer (GC) is the fourth most common type of neoplasm and the second cause of malignancy-related death across much of the world. Complex multi-factorial processes are involved in its genesis, classified in two determinant clusters: non-genetic and genetic . Variation in CDH1 gene expression may play an important role in increasing risk of diffuse and intestinal subtypes of GC. This tumor suppressor gene, located on chromosome 16q22.1, encodes a trans membrane glycoprotein called epithelial cadherin (E-cadherin). Materials and Methods: In this historical cohort study, from June 2004 to Journey 2005 we collected 50 samples from Kurdish patients with stage II pathologically diagnosed gastric cancer that underwent surgery. Tumor tissues were paraffin-embedded along with 54 control samples from non-ulcer dyspepsia (NUD) cases undergoing upper gastrointestinal endoscopy. Three biopsies were captured by endoscopy from each individual’s gastric antrum. Result: The mean age of the patients was 59.5±2 years. Some 23 cases (53.4%) had the CC genotype, 19 AC and 1 AA. H.pylori infection was noted in 30 patients (69%). Survival rates of gastric cancer patients were 90.7% in the first year, 39.5% in the second year and 6.9% in the third year. Female patients had higher survival rates (P=0.004). Conclusion: In this study we found that frequencies of -160(C>A) CDH1 genotypes were not comparable in H.pylori-infected and H.pylori-uninfected subjects in both case and control groups. These findings suggest that -160 (C>A) CDH1 polymorphism is not related with H.pylori infection susceptibility. In addition we found no significant relationship between the CDH1 -160(C/A) promoter polymorphism with predisposition to gastric cancer. Creative Commons Attribution License

Discovering More Accurate Frequent Web Usage Patterns

OpenAIRE

Bayir, Murat Ali; Toroslu, Ismail Hakki; Cosar, Ahmet; Fidan, Guven

2008-01-01

Web usage mining is a type of web mining, which exploits data mining techniques to discover valuable information from navigation behavior of World Wide Web users. As in classical data mining, data preparation and pattern discovery are the main issues in web usage mining. The first phase of web usage mining is the data processing phase, which includes the session reconstruction operation from server logs. Session reconstruction success directly affects the quality of the frequent patterns disc...

4G/5G polymorphism of plasminogen activator inhibitor-1 gene is associated with polycystic ovary syndrome in Chinese patients: a meta-analysis.

Science.gov (United States)

Wang, Li-Hong; Wang, Li-Mei; Zhou, Na

2015-09-01

To date, case-control studies on the association between a single-nucleotide polymorphism (SNP) in the plasminogen activator inhibitor-1 (PAI-1) gene and polycystic ovary syndrome (PCOS) have provided controversial results. The electronic databases PubMed, Embase, Web of Science, and CNKI (China National Knowledge Infrastructure) were searched for studies to include in the present meta-analysis. The fixed effects and random effects models showed that the 4G allele was associated with a risk of PCOS compared with the 5G allele in Chinese patients (OR = 2.05; 95 % CI = 1.56-2.69), but not in Caucasian patients (OR = 1.05; 95 % CI = 0.81-1.37). The contrast of homozygotes and the recessive and dominant models produced the same pattern of results as the allele contrast. Our pooled data suggest evidence for a major role of PAI-1 gene 4G/5G polymorphism in the pathogenesis of PCOS among Chinese patients.

Do usage and scientific collaboration associate with citation impact

Energy Technology Data Exchange (ETDEWEB)

Chi, P.S.; Glänzel, W.

2016-07-01

In this study usage counts and times cited from Web of Science Core Collection (WoS) were collected for each article published in 2013 with Belgian, Israeli and Iranian addresses. We investigate the relations among three indicators related to citation impact, usage counts coauthorship, respectively. In addition, we apply the method of Characteristic Scores and Scal (CSS) to analyse the distributions of citations and usage counts. The results show that citations and usage counts in WoS correlate to each other significantly, especially in the social sciences. However, the increase of the number of co-authors does not increase usage counts or citations significantly. Furthermore, the stability of CSS-class distributions proves the availability of CSS in characterising both usage and citation distributions. (Author)

Actionable gene-based classification toward precision medicine in gastric cancer

Directory of Open Access Journals (Sweden)

Hiroshi Ichikawa

2017-10-01

Full Text Available Abstract Background Intertumoral heterogeneity represents a significant hurdle to identifying optimized targeted therapies in gastric cancer (GC. To realize precision medicine for GC patients, an actionable gene alteration-based molecular classification that directly associates GCs with targeted therapies is needed. Methods A total of 207 Japanese patients with GC were included in this study. Formalin-fixed, paraffin-embedded (FFPE tumor tissues were obtained from surgical or biopsy specimens and were subjected to DNA extraction. We generated comprehensive genomic profiling data using a 435-gene panel including 69 actionable genes paired with US Food and Drug Administration-approved targeted therapies, and the evaluation of Epstein-Barr virus (EBV infection and microsatellite instability (MSI status. Results Comprehensive genomic sequencing detected at least one alteration of 435 cancer-related genes in 194 GCs (93.7% and of 69 actionable genes in 141 GCs (68.1%. We classified the 207 GCs into four The Cancer Genome Atlas (TCGA subtypes using the genomic profiling data; EBV (N = 9, MSI (N = 17, chromosomal instability (N = 119, and genomically stable subtype (N = 62. Actionable gene alterations were not specific and were widely observed throughout all TCGA subtypes. To discover a novel classification which more precisely selects candidates for targeted therapies, 207 GCs were classified using hypermutated phenotype and the mutation profile of 69 actionable genes. We identified a hypermutated group (N = 32, while the others (N = 175 were sub-divided into six clusters including five with actionable gene alterations: ERBB2 (N = 25, CDKN2A, and CDKN2B (N = 10, KRAS (N = 10, BRCA2 (N = 9, and ATM cluster (N = 12. The clinical utility of this classification was demonstrated by a case of unresectable GC with a remarkable response to anti-HER2 therapy in the ERBB2 cluster. Conclusions This actionable gene

Preparation and characterization of Bi26-2xMn2xMo10O69-d and Bi26.4Mn0.6Mo10-2yMe2yO69-d (Me = V, Fe Solid Solutions

Directory of Open Access Journals (Sweden)

Z. A. Mikhaylovskaya

2017-09-01

Full Text Available Single phase samples of bismuth molybdate, Bi26Mo10O69, doped with Mn on the bismuth sublattice and V, Fe on the molybdenum sublattice were found to crystallize in the triclinic Bi26Mo10O69 structure at low doping levels and in the monoclinic Bi26Mo10O69 structure - at higher dopant concentration. The assumption that all Mn ions have an oxidation state of +2 was confirmed by means of magnetic measurement results analysis using Curie-Weiss law. Conductivity was investigated using impedance spectroscopy. The conductivity of Bi26.4Mn0.6Mo9.6Fe0.4O69-d was 1.2*10-2 S*cm-1 at 973 K and 2.2*10-4 S*cm-1 at 623 K, and the conductivity of Bi26.4Mn0.6Mo9.2V0.8O69-d was 2.2*10-3 S*cm-1 at 973 K and 2.2*10-5 S*cm-1 at 623 K.

MESUR: USAGE-BASED METRICS OF SCHOLARLY IMPACT

Energy Technology Data Exchange (ETDEWEB)

BOLLEN, JOHAN [Los Alamos National Laboratory; RODRIGUEZ, MARKO A. [Los Alamos National Laboratory; VAN DE SOMPEL, HERBERT [Los Alamos National Laboratory

2007-01-30

The evaluation of scholarly communication items is now largely a matter of expert opinion or metrics derived from citation data. Both approaches can fail to take into account the myriad of factors that shape scholarly impact. Usage data has emerged as a promising complement to existing methods o fassessment but the formal groundwork to reliably and validly apply usage-based metrics of schlolarly impact is lacking. The Andrew W. Mellon Foundation funded MESUR project constitutes a systematic effort to define, validate and cross-validate a range of usage-based metrics of schlolarly impact by creating a semantic model of the scholarly communication process. The constructed model will serve as the basis of a creating a large-scale semantic network that seamlessly relates citation, bibliographic and usage data from a variety of sources. A subsequent program that uses the established semantic network as a reference data set will determine the characteristics and semantics of a variety of usage-based metrics of schlolarly impact. This paper outlines the architecture and methodology adopted by the MESUR project and its future direction.

Determination of Toll-Like Receptor 1 Gene Polymorphisms in Zavot, Turkish Grey, East Anatolian Red, Anatolian Black and South Anatolian Red Cattle Breeds

OpenAIRE

Mehmet Ulaş Çınar; Korhan Arslan; Esma Gamze Ilgar; Bilal Akyüz

2016-01-01

Toll-like receptors (TLRs) play an important role in non-specific immunity against different infectious agents such as bacterium or parasite. The aim of this work was to investigate the allele and genotype frequencies of three single-nucleotide polymorphisms (SNPs) in bovine TLR1 gene in native Turkish cattle breeds. DNA samples were extracted using the phenol chloroform protocol from 77 Zavot, 60 Turkish Grey, 51 East Anatolian Red, 69 Anatolian Black and 46 South Anatolian Red cattle. Targe...

EFFECT OF YAM STORAGE TECHNIQUES USAGE ON FARM ...

African Journals Online (AJOL)

IBUKUN

1Department of Agricultural Economics and Farm Management, Faculty of ... significant effect on the usage of yam storage techniques, while access to credit ..... study area at subsidized rates so as to encourage them to use such techniques.

Nuclear magnetic moment of 69As from on-line β-NMR on oriented nuclei

International Nuclear Information System (INIS)

Golovko, V.V.; Kraev, I.S.; Phalet, T.; Severijns, N.; Delaure, B.; Beck, M.; Kozlov, V.Yu.; Lindroth, A.; Coeck, S.; Zakoucky, D.; Venos, D.; Srnka, D.; Honusek, M.; Herzog, P.; Tramm, C.; Koester, U.

2005-01-01

A precise value for the magnetic moment of the 69 As 5/2 - ground state has been obtained from nuclear magnetic resonance on oriented nuclei (NMR/ON) using the NICOLE 3 He- 4 He dilution refrigerator setup at ISOLDE/CERN. The NMR/ON signal was observed by monitoring the anisotropy of the 69 As β particles. The center frequency ν[B ext =0.0994(10)T]=169.98(9) MHz corresponds to μ[ 69 As]=+1.6229(16)μ N . This result differs considerably from the πf 5/2 single-particle value obtained with g factors for a free proton but is in reasonable agreement with the value obtained with effective g factors and with values from a core polarization calculation and from calculations in the framework of the interacting boson-fermion model. Assuming a single exponential spin-lattice relaxation behavior a relaxation time T 1 ' =10(25) s was observed for 69 AsFe -bar at a temperature of about 20 mK in a magnetic field B=0.1 T

Problematic Internet Usage of ICT Teachers

Science.gov (United States)

Gunduz, Semseddin

2017-01-01

Information and communication technologies (ICT) have affected all area in a society. Human can learn quickly and accurately from the internet. The aim of this study was to investigate what the problematic internet usage of ICT teachers. Therefore, the present study investigated the problematic internet usage, who worked as an ICT teacher in…

HLA-DPβ1 Asp84-Lys69 antigen-binding signature predicts event-free survival in childhood B-cell precursor acute lymphoblastic leukaemia: results from the MRC UKALL XI childhood ALL trial.

Science.gov (United States)

Taylor, G M; Wade, R; Hussain, A; Thompson, P; Hann, I; Gibson, B; Eden, T; Richards, S

2012-07-01

We previously reported that children in the UKALL XI ALL trial with HLA-DP 1 and -DP 3 supertypes had significantly worse event-free survival (EFS) than children with other DP supertypes. As DP 1 and DP 3 share two of four key antigen-binding amino-acid polymorphisms (aspartic acid84-lysine69), we asked whether Asp84-Lys69 or Asp84 alone were independent prognostic indicators in childhood acute lymphoblastic leukemia (ALL). We analysed EFS in 798 UKALL XI patients, stratified by Asp84-Lys69 vs non-Asp84-Lys69, for a median follow-up of 12.5 years. Asp84-Lys69 was associated with a significantly worse EFS than non-Asp84-Lys69 (5-year EFS: Asp84-Lys69: 58.8% (95% CI (confidence of interval): 52.7-64.9%); non-Asp84-Lys69: 67.3% (63.4-71.2%); 2P=0.007). Post-relapse EFS was 10% less in Asp84-Lys69 than non-Asp84-Lys69 patients. EFS was significantly worse (P=0.03) and post-relapse EFS marginally worse (P=0.06) in patients with Asp84 compared with Gly84. These results suggest that Asp84-Lys69 predicted adverse EFS in the context of UKALL XI because of Asp84, and may have influenced post-relapse EFS. We speculate that this may be due to the recruitment of Asp84-Lys69-restricted regulatory T cells in the context of this regimen, leading to the re-emergence of residual disease. However, functional and molecular studies of the prognostic value of this and other HLA molecular signatures in other childhood ALL trials are needed.

Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models.

Science.gov (United States)

Mahony, Shaun; McInerney, James O; Smith, Terry J; Golden, Aaron

2004-03-05

Many current gene prediction methods use only one model to represent protein-coding regions in a genome, and so are less likely to predict the location of genes that have an atypical sequence composition. It is likely that future improvements in gene finding will involve the development of methods that can adequately deal with intra-genomic compositional variation. This work explores a new approach to gene-prediction, based on the Self-Organizing Map, which has the ability to automatically identify multiple gene models within a genome. The current implementation, named RescueNet, uses relative synonymous codon usage as the indicator of protein-coding potential. While its raw accuracy rate can be less than other methods, RescueNet consistently identifies some genes that other methods do not, and should therefore be of interest to gene-prediction software developers and genome annotation teams alike. RescueNet is recommended for use in conjunction with, or as a complement to, other gene prediction methods.

Genetic Factors that Affect Tumorigenesis in NF1

National Research Council Canada - National Science Library

Stephens, Karen

2003-01-01

...) that flank the NF1 gene. We identified recombination hotspots where 69% of NF1 microdeletions occur and developed robust and sensitive assays to detect microdeletions in a patient blood sample...

Genetic Factors that Affect Tumorigenesis in NF1

National Research Council Canada - National Science Library

Stephens, Karen G

2004-01-01

...) that flank the NF1 gene. We identified recombination hotspots where 69% of NF1 microdeletions occur and developed robust and sensitive assays to detect microdeletions in a patient blood sample...

50 CFR 600.910 - Definitions and word usage.

Science.gov (United States)

2010-10-01

... 50 Wildlife and Fisheries 8 2010-10-01 2010-10-01 false Definitions and word usage. 600.910..., Consultation, and Recommendations § 600.910 Definitions and word usage. (a) Definitions. In addition to the... undertaken by a state agency. (b) Word usage. The terms “must”, “shall”, “should”, “may”, “may not”, “will...

50 CFR 600.810 - Definitions and word usage.

Science.gov (United States)

2010-10-01

... 50 Wildlife and Fisheries 8 2010-10-01 2010-10-01 false Definitions and word usage. 600.810...) § 600.810 Definitions and word usage. (a) Definitions. In addition to the definitions in the Magnuson...-Stevens Act. (b) Word usage. The terms “must”, “shall”, “should”, “may”, “may not”, “will”, “could”, and...

The impact of intragenic CpG content on gene expression.

Science.gov (United States)

Bauer, Asli Petra; Leikam, Doris; Krinner, Simone; Notka, Frank; Ludwig, Christine; Längst, Gernot; Wagner, Ralf

2010-07-01

The development of vaccine components or recombinant therapeutics critically depends on sustained expression of the corresponding transgene. This study aimed to determine the contribution of intragenic CpG content to expression efficiency in transiently and stably transfected mammalian cells. Based upon a humanized version of green fluorescent protein (GFP) containing 60 CpGs within its coding sequence, a CpG-depleted variant of the GFP reporter was established by carefully modulating the codon usage. Interestingly, GFP reporter activity and detectable protein amounts in stably transfected CHO and 293 cells were significantly decreased upon CpG depletion and independent from promoter usage (CMV, EF1 alpha). The reduction in protein expression associated with CpG depletion was likewise observed for other unrelated reporter genes and was clearly reflected by a decline in mRNA copy numbers rather than translational efficiency. Moreover, decreased mRNA levels were neither due to nuclear export restrictions nor alternative splicing or mRNA instability. Rather, the intragenic CpG content influenced de novo transcriptional activity thus implying a common transcription-based mechanism of gene regulation via CpGs. Increased high CpG transcription correlated with changed nucleosomal positions in vitro albeit histone density at the two genes did not change in vivo as monitored by ChIP.

CloudMonitor: Profiling Power Usage

OpenAIRE

Smith, James William; Khajeh-Hosseini, Ali; Ward, Jonathan Stuart; Sommerville, Ian

2012-01-01

In Cloud Computing platforms the addition of hardware monitoring devices to gather power usage data can be impractical or uneconomical due to the large number of machines to be metered. CloudMonitor, a monitoring tool that can generate power models for software-based power estimation, can provide insights to the energy costs of deployments without additional hardware. Accurate power usage data leads to the possibility of Cloud providers creating a separate tariff for power and therefore incen...

The Scope of Usage-based Theory

Directory of Open Access Journals (Sweden)

Paul eIbbotson

2013-05-01

Full Text Available Usage-based approaches typically draw on a relatively small set of cognitive processes, such as categorization, analogy and chunking to explain language structure and function. The goal of this paper is to first review the extent to which the ‘cognitive commitment’ of usage-based theory has had success in explaining empirical findings across domains, including language acquisition, processing and typology. We then look at the overall strengths and weaknesses of usage-based theory and highlight where there are significant debates. Finally, we draw special attention to a set of culturally generated structural patterns that seem to lie beyond the explanation of core usage-based cognitive processes. In this context we draw a distinction between cognition permitting language structure versus cognition entailing language structure. As well as addressing the need for greater clarity on the mechanisms of generalizations and the fundamental units of grammar, we suggest that integrating culturally generated structures within existing cognitive models of use will generate tighter predictions about how language works.

Usage of U7 snRNA in gene therapy of hemoglobin C disorder ...

African Journals Online (AJOL)

Here, a bioinformatic analysis was performed to study the effect of co-expression between human Hb C b-globin chain gene and U7.623. The gene ontological results show that full recovery of hemoglobin function and biological process can be derived. This confirms that U7 snRNA can be a good tool for gene therapy in Hb ...

Analysis of IgV gene mutations in B cell chronic lymphocytic leukaemia according to antigen-driven selection identifies subgroups with different prognosis and usage of the canonical somatic hypermutation machinery.

Science.gov (United States)

Degan, Massimo; Bomben, Riccardo; Bo, Michele Dal; Zucchetto, Antonella; Nanni, Paola; Rupolo, Maurizio; Steffan, Agostino; Attadia, Vincenza; Ballerini, Pier Ferruccio; Damiani, Daniela; Pucillo, Carlo; Poeta, Giovanni Del; Colombatti, Alfonso; Gattei, Valter

2004-07-01

Cases of B-cell chronic lymphocytic leukaemia (B-CLL) with mutated (M) IgV(H) genes have a better prognosis than unmutated (UM) cases. We analysed the IgV(H) mutational status of B-CLL according to the features of a canonical somatic hypermutation (SHM) process, correlating this data with survival. In a series of 141 B-CLLs, 124 cases were examined for IgV(H) gene per cent mutations and skewing of replacement/silent mutations in the framework/complementarity-determining regions as evidence of antigen-driven selection; this identified three B-CLL subsets: significantly mutated (sM), with evidence of antigen-driven selection, not significantly mutated (nsM) and UM, without such evidence and IgV(H) gene per cent mutations above or below the 2% cut-off. sM B-CLL patients had longer survival within the good prognosis subgroup that had more than 2% mutations of IgV(H) genes. sM, nsM and UM B-CLL were also characterized for the biased usage of IgV(H) families, intraclonal IgV(H) gene diversification, preference of mutations to target-specific nucleotides or hotspots, and for the expression of enzymes involved in SHM (translesion DNA polymerase zeta and eta and activation-induced cytidine deaminase). These findings indicate the activation of a canonical SHM process in nsM and sM B-CLLs and underscore the role of the antigen in defining the specific clinical and biological features of B-CLL.

High school students’ usage behavior and views about mobile phones

Directory of Open Access Journals (Sweden)

Ahmet Ergin

2014-09-01

Full Text Available Objective: The aim of this study was to determine high school students’ usage behavior and views about mobile phones. Methods:Totally 253 (85.5% students educated at Honaz High School within the academic year 2010-2011, participated to this cross-sectional study and a questionnaire consisting of 42 questions which aimed to determine usage behavior and views about mobile phones was administered to the students. Results:The mean age of the students was 16.1 ± 1.1 years, and 56.9% of them were girl. 79.8% of students have mobile phone and 53.9% of them make daily average of over 30 minutes mobile phone calls. 76.1% of participants stated that they did not use headphones, 78.1% did not turn off their mobile phones when they are sleeping and 67.3% put it right next to them or under the pillow. 83.1% of students think mobile phones are harmful for human health, 56.7% think the base stations are harmful to human health and the environment, 91.3% think mobile phones are harmful for children, pregnant women and elderly people. Conclusion: It is found that students’ mobile phone ownership is widespread, the age of starting to use mobile phone and headphones usage is low, knowledge about the base stations is not adequate.

The strategy of fusion genes construction determines efficient expression of introduced transcription factors.

Science.gov (United States)

Adamus, Tomasz; Konieczny, Paweł; Sekuła, Małgorzata; Sułkowski, Maciej; Majka, Marcin

2014-01-01

The main goal in gene therapy and biomedical research is an efficient transcription factors (TFs) delivery system. SNAIL, a zinc finger transcription factor, is strongly involved in tumor, what makes its signaling pathways an interesting research subject. The necessity of tracking activation of intracellular pathways has prompted fluorescent proteins usage as localization markers. Advanced molecular cloning techniques allow to generate fusion proteins from fluorescent markers and transcription factors. Depending on fusion strategy, the protein expression levels and nuclear transport ability are significantly different. The P2A self-cleavage motif through its cleavage ability allows two single proteins to be simultaneously expressed. The aim of this study was to compare two strategies for introducing a pair of genes using expression vector system. We have examined GFP and SNAI1 gene fusions by comprising common nucleotide polylinker (multiple cloning site) or P2A motif in between them, resulting in one fusion or two independent protein expressions respectively. In each case transgene expression levels and translation efficiency as well as nuclear localization of expressed protein have been analyzed. Our data showed that usage of P2A motif provides more effective nuclear transport of SNAIL transcription factor than conventional genes linker. At the same time the fluorescent marker spreads evenly in subcellular space.

Usage evaluation of the Physiotherapy Evidence Database (PEDro) among Brazilian physical therapists.

Science.gov (United States)

Elkins, Mark R; Moseley, Anne M; Pinto, Rafael Z

2015-01-01

It is unclear whether the Physiotherapy Evidence Database (PEDro) is widely and equally used by physical therapists in Brazil. As PEDro is considered a key resource to support evidence-based physical therapy, analyses of PEDro usage could reflect the extent of dissemination of evidence-based practice. To describe the usage of PEDro among the five regions of the World Confederation for Physical Therapy (WCPT) and, in more detail, in the South American region and Brazil over a 5-year period. PEDro home-page sessions and the number of searches performed were logged for a 5-year period (2010-2014). Absolute usage and relative usage were calculated for each region of the WCPT, each country in the South American region of WCPT, and each Regional Council (CREFITO) in Brazil. Europe had the highest absolute and relative usage among the five regions of the WCPT (971 searches per million-population per year), with the South American region ranked 4th in absolute terms and 3rd in relative terms (486). Within the South American region, Brazil accounted for nearly 60% of searches (755). Analysis at a national level revealed that usage per physical therapist in Brazil is very low across all CREFITOs. The highest usage occurred in CREFITO 6 with 1.3 searches per physical therapist per year. PEDro is not widely and equally used throughout Brazil. Strategies to promote PEDro and to make PEDro more accessible to physical therapists speaking Portuguese are needed.

Clock gene modulates roles of OXTR and AVPR1b genes in prosociality.

Directory of Open Access Journals (Sweden)

Haipeng Ci

Full Text Available BACKGROUND: The arginine vasopressin receptor (AVPR and oxytocin receptor (OXTR genes have been demonstrated to contribute to prosocial behavior. Recent research has focused on the manner by which these simple receptor genes influence prosociality, particularly with regard to the AVP system, which is modulated by the clock gene. The clock gene is responsible for regulating the human biological clock, affecting sleep, emotion and behavior. The current study examined in detail whether the influences of the OXTR and AVPR1b genes on prosociality are dependent on the clock gene. METHODOLOGY/PRINCIPAL FINDINGS: This study assessed interactions between the clock gene (rs1801260, rs6832769 and the OXTR (rs1042778, rs237887 and AVPR1b (rs28373064 genes in association with individual differences in prosociality in healthy male Chinese subjects (n = 436. The Prosocial Tendencies Measure (PTM-R was used to assess prosociality. Participants carrying both the GG/GA variant of AVPR1b rs28373064 and the AA variant of clock rs6832769 showed the highest scores on the Emotional PTM. Carriers of both the T allele of OXTR rs1042778 and the C allele of clock rs1801260 showed the lowest total PTM scores compared with the other groups. CONCLUSIONS: The observed interaction effects provide converging evidence that the clock gene and OXT/AVP systems are intertwined and contribute to human prosociality.

Clock gene modulates roles of OXTR and AVPR1b genes in prosociality.

Science.gov (United States)

Ci, Haipeng; Wu, Nan; Su, Yanjie

2014-01-01

The arginine vasopressin receptor (AVPR) and oxytocin receptor (OXTR) genes have been demonstrated to contribute to prosocial behavior. Recent research has focused on the manner by which these simple receptor genes influence prosociality, particularly with regard to the AVP system, which is modulated by the clock gene. The clock gene is responsible for regulating the human biological clock, affecting sleep, emotion and behavior. The current study examined in detail whether the influences of the OXTR and AVPR1b genes on prosociality are dependent on the clock gene. This study assessed interactions between the clock gene (rs1801260, rs6832769) and the OXTR (rs1042778, rs237887) and AVPR1b (rs28373064) genes in association with individual differences in prosociality in healthy male Chinese subjects (n = 436). The Prosocial Tendencies Measure (PTM-R) was used to assess prosociality. Participants carrying both the GG/GA variant of AVPR1b rs28373064 and the AA variant of clock rs6832769 showed the highest scores on the Emotional PTM. Carriers of both the T allele of OXTR rs1042778 and the C allele of clock rs1801260 showed the lowest total PTM scores compared with the other groups. The observed interaction effects provide converging evidence that the clock gene and OXT/AVP systems are intertwined and contribute to human prosociality.

Health insurance, neighborhood income, and emergency department usage by Utah children 1996–1998

Directory of Open Access Journals (Sweden)

Knight Stacey

2005-04-01

Full Text Available Abstract Background It is estimated that approximately half of emergency department (ED usage in the U.S. and other developed countries is for non-urgent conditions and that this usage is related to availability, social, and economic factors. We examined pediatric ED usage in a U.S. state with respect to income, health insurance status, types of medical conditions, and whether introduction of managed care affected utilization by Medicaid children. Methods Emergency department usage rates were calculated from 1996 through 1998 using Utah ED data for children with commercial health insurance, Medicaid, for uninsured children, and by income group estimating neighborhood household income from Zip code of residence. We analyzed usage following the July 1996 transition of Utah Medicaid to managed care. Results Children with Medicaid had approximately 50% greater ED utilization rates than children with commercial health insurance or uninsured children. The majority of usage for Medicaid and uninsured children was for non-traumatic conditions. Only 35% of total ED usage was for non-emergent or non-urgent conditions and this was related to both Medicaid and low household income. Children lacking health insurance were more likely to be discharged against medical advice (OR = 2.36, 95% C.I. 1.88–2.96. There was no reduction in Medicaid ED usage following the transition to managed care. Conclusion Usage of ED services is related to both health insurance status and income. Children lacking health insurance and Medicaid children have excessive usage for conditions which could be treated in a primary care setting. That managed care does not reduce Medicaid ED usage is consistent with findings of other studies.

highroad Is a Carboxypetidase Induced by Retinoids to Clear Mutant Rhodopsin-1 in Drosophila Retinitis Pigmentosa Models

Directory of Open Access Journals (Sweden)

Huai-Wei Huang

2018-02-01

Full Text Available Rhodopsins require retinoid chromophores for their function. In vertebrates, retinoids also serve as signaling molecules, but whether these molecules similarly regulate gene expression in Drosophila remains unclear. Here, we report the identification of a retinoid-inducible gene in Drosophila, highroad, which is required for photoreceptors to clear folding-defective mutant Rhodopsin-1 proteins. Specifically, knockdown or genetic deletion of highroad blocks the degradation of folding-defective Rhodopsin-1 mutant, ninaEG69D. Moreover, loss of highroad accelerates the age-related retinal degeneration phenotype of ninaEG69D mutants. Elevated highroad transcript levels are detected in ninaEG69D flies, and interestingly, deprivation of retinoids in the fly diet blocks this effect. Consistently, mutations in the retinoid transporter, santa maria, impairs the induction of highroad in ninaEG69D flies. In cultured S2 cells, highroad expression is induced by retinoic acid treatment. These results indicate that cellular quality-control mechanisms against misfolded Rhodopsin-1 involve regulation of gene expression by retinoids.

PPB | What is the DICER1 gene?

Science.gov (United States)

DICER1 is a gene that manages the function of other genes. Inherited changes in DICER1 can result in a variety of tumors, including pleuropulmonary blastoma (PPB). The PPB DICER1 Syndrome Study ‹an observational clinical research study is enrolling children with PPB and their families.

47 CFR 69.119 - Basic service element expedited approval process.

Science.gov (United States)

2010-10-01

... 47 Telecommunication 3 2010-10-01 2010-10-01 false Basic service element expedited approval process. 69.119 Section 69.119 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES (CONTINUED) ACCESS CHARGES Computation of Charges § 69.119 Basic service element...

East African Agricultural and Forestry Journal - Vol 69 (2003)

African Journals Online (AJOL)

Emergence of forage legume seedlings influenced by water potential and soil strength · EMAIL FULL TEXT EMAIL FULL TEXT · DOWNLOAD FULL TEXT DOWNLOAD FULL TEXT. DMG Njarui, LM Bahnisch, B O'Hagan, B So, 29-38. http://dx.doi.org/10.4314/eaafj.v69i1.1803 ...

Evolutionary and genetic analysis of the VP2 gene of canine parvovirus.

Science.gov (United States)

Li, Gairu; Ji, Senlin; Zhai, Xiaofeng; Zhang, Yuxiang; Liu, Jie; Zhu, Mengyan; Zhou, Jiyong; Su, Shuo

2017-07-17

Canine parvovirus (CPV) type 2 emerged in 1978 in the USA and quickly spread among dog populations all over the world with high morbidity. Although CPV is a DNA virus, its genomic substitution rate is similar to some RNA viruses. Therefore, it is important to trace the evolution of CPV to monitor the appearance of mutations that might affect vaccine effectiveness. Our analysis shows that the VP2 genes of CPV isolated from 1979 to 2016 are divided into six groups: GI, GII, GIII, GIV, GV, and GVI. Amino acid mutation analysis revealed several undiscovered important mutation sites: F267Y, Y324I, and T440A. Of note, the evolutionary rate of the CPV VP2 gene from Asia and Europe decreased. Codon usage analysis showed that the VP2 gene of CPV exhibits high bias with an ENC ranging from 34.93 to 36.7. Furthermore, we demonstrate that natural selection plays a major role compared to mutation pressure driving CPV evolution. There are few studies on the codon usage of CPV. Here, we comprehensively studied the genetic evolution, codon usage pattern, and evolutionary characterization of the VP2 gene of CPV. The novel findings revealing the evolutionary process of CPV will greatly serve future CPV research.

An updated assessment of social media usage by dermatology journals and organizations.

Science.gov (United States)

Patel, Ravi R; Hill, Mary K; Smith, Mallory K; Seeker, Paige; Dellavalle, Robert P

2018-02-15

Despite the increasing prevalence of social media usage, the activity of dermatology journals and professional and patient-centered organizations on top social media platforms has not been investigated since 2012. We investigated a total of 124 dermatology journals, 242 professional organizations, and 78 patient-centered organizations to assess their presence and popularity on social media. Searches were conducted to identify journals and organizations on Facebook and Twitter. Similar searches were done for organizations on LinkedIn. The number of Facebook likes, Twitter followers, and LinkedIn followers of the dermatological entities were quantified. There were 22 (17.7%) dermatology journals active on Facebook and 21 (16.9%) on Twitter. Amongst the professional organizations, 114 (47.1%) were on Facebook, 69 (28.5%) on Twitter, and 50 (20.7%) on LinkedIn. In comparison, 68 (87.2%) patient-centered organizations were on Facebook, 56 (71.8%) on Twitter, and 56 (71.8%) on LinkedIn. Our results demonstrate that the popularity of dermatology journals and professional and patient-centered organizations on top social networking sites has grown markedly since 2012. Although the number of dermatology journals on social media has increased since 2012, their presence continues to trail behind professional and patient-centered dermatological organizations, suggesting underutilization of a valuable resource.

LHCb Computing Resource usage in 2017

CERN Document Server

Bozzi, Concezio

2018-01-01

This document reports the usage of computing resources by the LHCb collaboration during the period January 1st – December 31st 2017. The data in the following sections have been compiled from the EGI Accounting portal: https://accounting.egi.eu. For LHCb specific information, the data is taken from the DIRAC Accounting at the LHCb DIRAC Web portal: http://lhcb-portal-dirac.cern.ch.

RNAi-Based Identification of Gene-Specific Nuclear Cofactor Networks Regulating Interleukin-1 Target Genes

Directory of Open Access Journals (Sweden)

Johanna Meier-Soelch

2018-04-01

Full Text Available The potent proinflammatory cytokine interleukin (IL-1 triggers gene expression through the NF-κB signaling pathway. Here, we investigated the cofactor requirements of strongly regulated IL-1 target genes whose expression is impaired in p65 NF-κB-deficient murine embryonic fibroblasts. By two independent small-hairpin (shRNA screens, we examined 170 genes annotated to encode nuclear cofactors for their role in Cxcl2 mRNA expression and identified 22 factors that modulated basal or IL-1-inducible Cxcl2 levels. The functions of 16 of these factors were validated for Cxcl2 and further analyzed for their role in regulation of 10 additional IL-1 target genes by RT-qPCR. These data reveal that each inducible gene has its own (quantitative requirement of cofactors to maintain basal levels and to respond to IL-1. Twelve factors (Epc1, H2afz, Kdm2b, Kdm6a, Mbd3, Mta2, Phf21a, Ruvbl1, Sin3b, Suv420h1, Taf1, and Ube3a have not been previously implicated in inflammatory cytokine functions. Bioinformatics analysis indicates that they are components of complex nuclear protein networks that regulate chromatin functions and gene transcription. Collectively, these data suggest that downstream from the essential NF-κB signal each cytokine-inducible target gene has further subtle requirements for individual sets of nuclear cofactors that shape its transcriptional activation profile.

Comparative study of the hemagglutinin and neuraminidase genes of influenza A virus H3N2, H9N2, and H5N1 subtypes using bioinformatics techniques.

Science.gov (United States)

Ahn, Insung; Son, Hyeon S

2007-07-01

To investigate the genomic patterns of influenza A virus subtypes, such as H3N2, H9N2, and H5N1, we collected 1842 sequences of the hemagglutinin and neuraminidase genes from the NCBI database and parsed them into 7 categories: accession number, host species, sampling year, country, subtype, gene name, and sequence. The sequences that were isolated from the human, avian, and swine populations were extracted and stored in a MySQL database for intensive analysis. The GC content and relative synonymous codon usage (RSCU) values were calculated using JAVA codes. As a result, correspondence analysis of the RSCU values yielded the unique codon usage pattern (CUP) of each subtype and revealed no extreme differences among the human, avian, and swine isolates. H5N1 subtype viruses exhibited little variation in CUPs compared with other subtypes, suggesting that the H5N1 CUP has not yet undergone significant changes within each host species. Moreover, some observations may be relevant to CUP variation that has occurred over time among the H3N2 subtype viruses isolated from humans. All the sequences were divided into 3 groups over time, and each group seemed to have preferred synonymous codon patterns for each amino acid, especially for arginine, glycine, leucine, and valine. The bioinformatics technique we introduce in this study may be useful in predicting the evolutionary patterns of pandemic viruses.

2011 Radioactive Materials Usage Survey for Unmonitored Point Sources

Energy Technology Data Exchange (ETDEWEB)

Sturgeon, Richard W. [Los Alamos National Laboratory

2012-06-27

This report provides the results of the 2011 Radioactive Materials Usage Survey for Unmonitored Point Sources (RMUS), which was updated by the Environmental Protection (ENV) Division's Environmental Stewardship (ES) at Los Alamos National Laboratory (LANL). ES classifies LANL emission sources into one of four Tiers, based on the potential effective dose equivalent (PEDE) calculated for each point source. Detailed descriptions of these tiers are provided in Section 3. The usage survey is conducted annually; in odd-numbered years the survey addresses all monitored and unmonitored point sources and in even-numbered years it addresses all Tier III and various selected other sources. This graded approach was designed to ensure that the appropriate emphasis is placed on point sources that have higher potential emissions to the environment. For calendar year (CY) 2011, ES has divided the usage survey into two distinct reports, one covering the monitored point sources (to be completed later this year) and this report covering all unmonitored point sources. This usage survey includes the following release points: (1) all unmonitored sources identified in the 2010 usage survey, (2) any new release points identified through the new project review (NPR) process, and (3) other release points as designated by the Rad-NESHAP Team Leader. Data for all unmonitored point sources at LANL is stored in the survey files at ES. LANL uses this survey data to help demonstrate compliance with Clean Air Act radioactive air emissions regulations (40 CFR 61, Subpart H). The remainder of this introduction provides a brief description of the information contained in each section. Section 2 of this report describes the methods that were employed for gathering usage survey data and for calculating usage, emissions, and dose for these point sources. It also references the appropriate ES procedures for further information. Section 3 describes the RMUS and explains how the survey results are

Measurements of the total cross-section difference ΔδL (np) at 1.39, 1.69, 1.89 and 1.99 GeV

International Nuclear Information System (INIS)

Sharov, V.I.; Anishchenko, N.G.; Antonenko, V.G.

2004-01-01

New accurate results of the neutron-proton spin-dependent total cross-section difference Δδ L (np) at the neutron beam kinetic energies of 1.39, 1.69, 1.89 and 1.99 GeV are presented. In general these data complete the measurements of energy dependence of Δδ L (np) over the Dubna Synchrophasotron energy region. The quasi-monochromatic neutron beam was produced by break-up of extracted polarized deuterons. The deuteron (and hence neutron) polarization direction was flipped every accelerator burst. The neutron vertical direction of polarization was rotated onto the neutron beam direction and longitudinally (L) polarized neutrons were transmitted through the large proton L-polarized target. The longitudinal target polarization direction was inverted after 1-2 days of measurements. Four different combinations of the beam and target parallel and antiparallel polarization directions, both oriented along the neutron beam momentum, were used at each energy. A fast decrease of - Δδ L (np) with increasing energy above 1.1 GeV and a structure in the energy dependence around 1.8 GeV, first observed from our previous data, seem to be well revealed. The new results are also compared with model predictions and with phase shift analysis fits. The Δδ L quantities for isosinglet state I = 0, deduced from the measured Δδ L (np) values and known Δδ L (pp) data, are also given. The results of the measurements of unpolarized total cross sections δ 0tot (np) at 1.3, 1.4 and 1.5 GeV and δ 0tot (nC) at 1.4 and 1.5 GeV are presented as well. These data were obtained using the same apparatus and high intensity unpolarized deuteron beams extracted either from the Synchrophasotron, or from the Nuclotron

Cloud Usage Patterns : A Formalism for Description of Cloud Usage Scenarios

NARCIS (Netherlands)

Milenkoski, Aleksandar; Iosup, Alexandru; Kounev, Samuel; Sachs, Kai; Rygielski, Piotr; Ding, Jason; Cirne, Walfredo; Rosenberg, Florian

2014-01-01

Cloud computing is becoming an increasingly lucrative branch of the existing information and communication technologies (ICT). Enabling a debate about cloud usage scenarios can help with attracting new customers, sharing best-practices, and designing new cloud services. In contrast to previous

The genomic structure of the DMBT1 gene

DEFF Research Database (Denmark)

Mollenhauer, J; Holmskov, U; Wiemann, S

1999-01-01

Increasing evidence has accumulated for an involvement of the inactivation of tumour suppressor genes at chromosome 10q in the carcinogenesis of brain tumours, melanomas, and carcinomas of the lung, the prostate, the pancreas, and the endometrium. The gene DMBT1 (Deleted in Malignant Brain Tumours...... 1) is located at chromosome 10q25.3-q26.1, within one of the putative intervals for tumour suppressor genes. DMBT1 is a member of the scavenger-receptor cysteine-rich (SRCR) superfamily and displays homozygous deletions or lack of expression in glioblastoma multiforme, medulloblastoma......, and in gastrointestinal and lung cancers. Based on these properties, DMBT1 has been proposed to be a candidate tumour suppressor gene. We have determined the genomic sequence of DMBT1 to allow analyses of mutations. The gene has at least 54 exons that span a genomic region of about 80 kb. We have identified a putative...

[Gene doping--current possibilities, risks and means of prevention].

Science.gov (United States)

Pleger, N; Vitzthum, K; Schöffel, N; Quarcoo, D; Uibel, S; Groneberg, D A

2011-03-01

With the advances in gene therapy fears of an abuse in sports arise. The WADA's definition of the term strictly differentiates between gene doping and gene therapy. There are in vivo and ex vivo practices to manipulate the different phases of gene expression in the organism, with viral vectors being looked upon as the most efficient ones. IGF-1, PPARδ, MSTN and EPO play the most important roles in today's scientific research. Their potential was proven in various animal studies, showing a significant improvement of performances. Potential risks for human users include severe immune reactions, mutagenesis, and raised risk for cancer. Big efforts are being put into the development of ways of detection, however until now there are neither practicable methods of control nor any reported cases of manipulated humans. Still, a usage of gene doping that has already taken place cannot be ruled out and is highly likely. © Georg Thieme Verlag KG Stuttgart · New York.

Targeting the human lysozyme gene on bovine αs1- casein gene ...

African Journals Online (AJOL)

ajl yemi

2011-11-28

Nov 28, 2011 ... Targeting an exogenous gene into a favorable gene locus and for expression under endogenous regulators is ... case, the expression of human lysozyme could be regulated by the endogenous cis-element of αs1- casein gene in .... Mouse mammary epithelial C127 cells (Cell Bank, Chinese. Academy of ...

Alteration of the SETBP1 gene and splicing pathway genes SF3B1, U2AF1, and SRSF2 in childhood acute myeloid leukemia.

Science.gov (United States)

Choi, Hyun-Woo; Kim, Hye-Ran; Baek, Hee-Jo; Kook, Hoon; Cho, Duck; Shin, Jong-Hee; Suh, Soon-Pal; Ryang, Dong-Wook; Shin, Myung-Geun

2015-01-01

Recurrent somatic SET-binding protein 1 (SETBP1) and splicing pathway gene mutations have recently been found in atypical chronic myeloid leukemia and other hematologic malignancies. These mutations have been comprehensively analyzed in adult AML, but not in childhood AML. We investigated possible alteration of the SETBP1, splicing factor 3B subunit 1 (SF3B1), U2 small nuclear RNA auxiliary factor 1 (U2AF1), and serine/arginine-rich splicing factor 2 (SRSF2) genes in childhood AML. Cytogenetic and molecular analyses were performed to reveal chromosomal and genetic alterations. Sequence alterations in the SETBP1, SF3B1, U2AF1, and SRSF2 genes were examined by using direct sequencing in a cohort of 53 childhood AML patients. Childhood AML patients did not harbor any recurrent SETBP1 gene mutations, although our study did identify a synonymous mutation in one patient. None of the previously reported aberrations in the mutational hotspot of SF3B1, U2AF1, and SRSF2 were identified in any of the 53 patients. Alterations of the SETBP1 gene or SF3B1, U2AF1, and SRSF2 genes are not common genetic events in childhood AML, implying that the mutations are unlikely to exert a driver effect in myeloid leukemogenesis during childhood.

49 CFR 1242.69 - Clearing wrecks (account XX-52-63).

Science.gov (United States)

2010-10-01

... 49 Transportation 9 2010-10-01 2010-10-01 false Clearing wrecks (account XX-52-63). 1242.69 Section 1242.69 Transportation Other Regulations Relating to Transportation (Continued) SURFACE...-Transportation § 1242.69 Clearing wrecks (account XX-52-63). Separate common expenses according to specific...

Genetic polymorphisms in CYP1A1, GSTM1, GSTP1 and GSTT1 metabolic genes and risk of lung cancer in Asturias

International Nuclear Information System (INIS)

López-Cima, M Felicitas; Álvarez-Avellón, Sara M; Pascual, Teresa; Fernández-Somoano, Ana; Tardón, Adonina

2012-01-01

Metabolic genes have been associated with the function of metabolizing and detoxifying environmental carcinogens. Polymorphisms present in these genes could lead to changes in their metabolizing and detoxifying ability and thus may contribute to individual susceptibility to different types of cancer. We investigated if the individual and/or combined modifying effects of the CYP1A1 MspI T6235C, GSTM1 present/null, GSTT1 present/null and GSTP1 Ile105Val polymorphisms are related to the risk of developing lung cancer in relation to tobacco consumption and occupation in Asturias, Northern Spain. A hospital-based case–control study (CAPUA Study) was designed including 789 lung cancer patients and 789 control subjects matched in ethnicity, age, sex, and hospital. Genotypes were determined by PCR or PCR-RFLP. Individual and combination effects were analysed using an unconditional logistic regression adjusting for age, pack-years, family history of any cancer and occupation. No statistically significant main effects were observed for the carcinogen metabolism genes in relation to lung cancer risk. In addition, the analysis did not reveal any significant gene-gene, gene-tobacco smoking or gene-occupational exposure interactions relative to lung cancer susceptibility. Lastly, no significant gene-gene combination effects were observed. These results suggest that genetic polymorphisms in the CYP1A1, GSTM1, GSTT1 and GSTP1 metabolic genes were not significantly associated with lung cancer risk in the current study. The results of the analysis of gene-gene interactions of CYP1A1 MspI T6235C, GSTM1 present/null, GSTT1 present/null and GSTP1 Ile105Val polymorphisms in lung cancer risk indicate that these genes do not interact in lung cancer development

Gene polymorphisms and male infertility--a meta-analysis and literature review

DEFF Research Database (Denmark)

Tüttelmann, Frank; Rajpert-De Meyts, Ewa; Nieschlag, Eberhard

2007-01-01

(OR 1.81, 1.46-2.24 CI, PT (OR 1.39, 1.15-2.69 95% CI, P=0.0006) but not for POLG, DAZL, USP26 or FSHR. The influence of CAG repeat length in AR remains open and debated. Genes encoding nuclear proteins (PRM1/2, TNP1/2) and ER1 are possible candidates for further examination, while the role of TAF7L...

Synthesis of highly c-oriented ZIF-69 membranes by secondary growth and their gas permeation properties

KAUST Repository

Liu, Yunyang

2011-09-01

A seeded growth procedure was successfully developed to synthesize highly c-oriented and well-intergrown zeolitic imidazolate framework-69 (ZIF-69) membranes on porous α-alumina substrates. The synthesis conditions were optimized both for seed preparation and for secondary growth. For seeding, a facile method was developed to prepare smaller and flat ZIF-69 microcrystals in order to make thin and c-oriented seed layers. While for secondary growth, a synthesis condition that favored the growth along the c-direction was chosen in order to form highly c-oriented ZIF-69 membranes after growth. As a result, the majority of ZIF-69 grains inside the membrane have their straight channels along the crystallographic c-axis aligned perpendicularly to the substrate surface. Such alignment was confirmed by both XRD and pole figure analysis. The mixture-gas separation studies that were carried out at room temperature and 1atm gave separation factors of 6.3, 5.0, 4.6 for CO2/N2, CO2/CO and CO2/CH4 respectively, and a permeance of ∼1.0×10-7molm-2s-1Pa-1 for CO2 in almost all mixtures. Both the separation factor and permeance were better than the performance of the ZIF-69 membranes prepared by the in situ solvothermal method due to improvement in the membrane microstructure by the seeded growth method. © 2011 Elsevier B.V.

Synthesis of highly c-oriented ZIF-69 membranes by secondary growth and their gas permeation properties

KAUST Repository

Liu, Yunyang; Zeng, Gaofeng; Pan, Yichang; Lai, Zhiping

2011-01-01

A seeded growth procedure was successfully developed to synthesize highly c-oriented and well-intergrown zeolitic imidazolate framework-69 (ZIF-69) membranes on porous α-alumina substrates. The synthesis conditions were optimized both for seed preparation and for secondary growth. For seeding, a facile method was developed to prepare smaller and flat ZIF-69 microcrystals in order to make thin and c-oriented seed layers. While for secondary growth, a synthesis condition that favored the growth along the c-direction was chosen in order to form highly c-oriented ZIF-69 membranes after growth. As a result, the majority of ZIF-69 grains inside the membrane have their straight channels along the crystallographic c-axis aligned perpendicularly to the substrate surface. Such alignment was confirmed by both XRD and pole figure analysis. The mixture-gas separation studies that were carried out at room temperature and 1atm gave separation factors of 6.3, 5.0, 4.6 for CO2/N2, CO2/CO and CO2/CH4 respectively, and a permeance of ∼1.0×10-7molm-2s-1Pa-1 for CO2 in almost all mixtures. Both the separation factor and permeance were better than the performance of the ZIF-69 membranes prepared by the in situ solvothermal method due to improvement in the membrane microstructure by the seeded growth method. © 2011 Elsevier B.V.

Gene expression profile analysis of Ligon lintless-1 (Li1) mutant reveals important genes and pathways in cotton leaf and fiber development.

Science.gov (United States)

Ding, Mingquan; Jiang, Yurong; Cao, Yuefen; Lin, Lifeng; He, Shae; Zhou, Wei; Rong, Junkang

2014-02-10

Ligon lintless-1 (Li1) is a monogenic dominant mutant of Gossypium hirsutum (upland cotton) with a phenotype of impaired vegetative growth and short lint fibers. Despite years of research involving genetic mapping and gene expression profile analysis of Li1 mutant ovule tissues, the gene remains uncloned and the underlying pathway of cotton fiber elongation is still unclear. In this study, we report the whole genome-level deep-sequencing analysis of leaf tissues of the Li1 mutant. Differentially expressed genes in leaf tissues of mutant versus wild-type (WT) plants are identified, and the underlying pathways and potential genes that control leaf and fiber development are inferred. The results show that transcription factors AS2, YABBY5, and KANDI-like are significantly differentially expressed in mutant tissues compared with WT ones. Interestingly, several fiber development-related genes are found in the downregulated gene list of the mutant leaf transcriptome. These genes include heat shock protein family, cytoskeleton arrangement, cell wall synthesis, energy, H2O2 metabolism-related genes, and WRKY transcription factors. This finding suggests that the genes are involved in leaf morphology determination and fiber elongation. The expression data are also compared with the previously published microarray data of Li1 ovule tissues. Comparative analysis of the ovule transcriptomes of Li1 and WT reveals that a number of pathways important for fiber elongation are enriched in the downregulated gene list at different fiber development stages (0, 6, 9, 12, 15, 18dpa). Differentially expressed genes identified in both leaf and fiber samples are aligned with cotton whole genome sequences and combined with the genetic fine mapping results to identify a list of candidate genes for Li1. Copyright © 2013 Elsevier B.V. All rights reserved.

40 CFR 69.51 - Motor vehicle diesel fuel.

Science.gov (United States)

2010-07-01

... 40 Protection of Environment 15 2010-07-01 2010-07-01 false Motor vehicle diesel fuel. 69.51... (CONTINUED) SPECIAL EXEMPTIONS FROM REQUIREMENTS OF THE CLEAN AIR ACT Alaska § 69.51 Motor vehicle diesel... motor vehicle diesel fuel standards and dye provisions under 40 CFR 80.520 and associated requirements...

19 CFR 210.69 - Approval of complainant's temporary relief bond.

Science.gov (United States)

2010-04-01

... 19 Customs Duties 3 2010-04-01 2010-04-01 false Approval of complainant's temporary relief bond. 210.69 Section 210.69 Customs Duties UNITED STATES INTERNATIONAL TRADE COMMISSION INVESTIGATIONS OF UNFAIR PRACTICES IN IMPORT TRADE ADJUDICATION AND ENFORCEMENT Temporary Relief § 210.69 Approval of...

Library training to promote electronic resource usage

DEFF Research Database (Denmark)

Frandsen, Tove Faber; Tibyampansha, Dativa; Ibrahim, Glory

2017-01-01

Purpose: Increasing the usage of electronic resources is an issue of concern for many libraries all over the world. Several studies stress the importance of information literacy and instruction in order to increase the usage. Design/methodology/approach: The present article presents the results...

Cloning and sequencing of phenol oxidase 1 (pox1) gene from ...

African Journals Online (AJOL)

The gene (pox1) encoding a phenol oxidase 1 from Pleurotus ostreatus was sequenced and the corresponding pox1-cDNA was also synthesized, cloned and sequenced. The isolated gene is flanked by an upstream region called the promoter (399 bp) prior to the start codon (ATG). The putative metalresponsive elements ...

Genome-wide identification of KANADI1 target genes.

Directory of Open Access Journals (Sweden)

Paz Merelo

Full Text Available Plant organ development and polarity establishment is mediated by the action of several transcription factors. Among these, the KANADI (KAN subclade of the GARP protein family plays important roles in polarity-associated processes during embryo, shoot and root patterning. In this study, we have identified a set of potential direct target genes of KAN1 through a combination of chromatin immunoprecipitation/DNA sequencing (ChIP-Seq and genome-wide transcriptional profiling using tiling arrays. Target genes are over-represented for genes involved in the regulation of organ development as well as in the response to auxin. KAN1 affects directly the expression of several genes previously shown to be important in the establishment of polarity during lateral organ and vascular tissue development. We also show that KAN1 controls through its target genes auxin effects on organ development at different levels: transport and its regulation, and signaling. In addition, KAN1 regulates genes involved in the response to abscisic acid, jasmonic acid, brassinosteroids, ethylene, cytokinins and gibberellins. The role of KAN1 in organ polarity is antagonized by HD-ZIPIII transcription factors, including REVOLUTA (REV. A comparison of their target genes reveals that the REV/KAN1 module acts in organ patterning through opposite regulation of shared targets. Evidence of mutual repression between closely related family members is also shown.

A POTENTIAL SUPER-VENUS IN THE KEPLER-69 SYSTEM

International Nuclear Information System (INIS)

Kane, Stephen R.; Gelino, Dawn M.; Barclay, Thomas

2013-01-01

Transiting planets have greatly expanded and diversified the exoplanet field. These planets provide greater access to characterization of exoplanet atmospheres and structure. The Kepler mission has been particularly successful in expanding the exoplanet inventory, even to planets smaller than the Earth. The orbital period sensitivity of the Kepler data is now extending into the habitable zones of their host stars, and several planets larger than the Earth have been found to lie therein. Here we examine one such proposed planet, Kepler-69c. We provide new orbital parameters for this planet and an in-depth analysis of the habitable zone. We find that, even under optimistic conditions, this 1.7 R ⊕ planet is unlikely to be within the habitable zone of Kepler-69. Furthermore, the planet receives an incident flux of 1.91 times the solar constant, which is similar to that received by Venus. We thus suggest that this planet is likely a super-Venus rather than a super-Earth in terms of atmospheric properties and habitability, and we propose follow-up observations to disentangle the ambiguity.

A POTENTIAL SUPER-VENUS IN THE KEPLER-69 SYSTEM

Energy Technology Data Exchange (ETDEWEB)

Kane, Stephen R.; Gelino, Dawn M. [NASA Exoplanet Science Institute, Caltech, MS 100-22, 770 South Wilson Avenue, Pasadena, CA 91125 (United States); Barclay, Thomas, E-mail: skane@ipac.caltech.edu [NASA Ames Research Center, M/S 244-30, Moffett Field, CA 94035 (United States)

2013-06-20

Transiting planets have greatly expanded and diversified the exoplanet field. These planets provide greater access to characterization of exoplanet atmospheres and structure. The Kepler mission has been particularly successful in expanding the exoplanet inventory, even to planets smaller than the Earth. The orbital period sensitivity of the Kepler data is now extending into the habitable zones of their host stars, and several planets larger than the Earth have been found to lie therein. Here we examine one such proposed planet, Kepler-69c. We provide new orbital parameters for this planet and an in-depth analysis of the habitable zone. We find that, even under optimistic conditions, this 1.7 R{sub Circled-Plus} planet is unlikely to be within the habitable zone of Kepler-69. Furthermore, the planet receives an incident flux of 1.91 times the solar constant, which is similar to that received by Venus. We thus suggest that this planet is likely a super-Venus rather than a super-Earth in terms of atmospheric properties and habitability, and we propose follow-up observations to disentangle the ambiguity.

40 CFR 52.254 - Organic solvent usage.

Science.gov (United States)

2010-07-01

... 40 Protection of Environment 3 2010-07-01 2010-07-01 false Organic solvent usage. 52.254 Section...) APPROVAL AND PROMULGATION OF IMPLEMENTATION PLANS California § 52.254 Organic solvent usage. (a) This... (d) of this section and the architectural coatings and solvent disposal emission limitations...

Cielo Computational Environment Usage Model With Mappings to ACE Requirements for the General Availability User Environment Capabilities Release Version 1.1

Energy Technology Data Exchange (ETDEWEB)

Vigil,Benny Manuel [Los Alamos National Laboratory; Ballance, Robert [SNL; Haskell, Karen [SNL

2012-08-09

Cielo is a massively parallel supercomputer funded by the DOE/NNSA Advanced Simulation and Computing (ASC) program, and operated by the Alliance for Computing at Extreme Scale (ACES), a partnership between Los Alamos National Laboratory (LANL) and Sandia National Laboratories (SNL). The primary Cielo compute platform is physically located at Los Alamos National Laboratory. This Cielo Computational Environment Usage Model documents the capabilities and the environment to be provided for the Q1 FY12 Level 2 Cielo Capability Computing (CCC) Platform Production Readiness Milestone. This document describes specific capabilities, tools, and procedures to support both local and remote users. The model is focused on the needs of the ASC user working in the secure computing environments at Lawrence Livermore National Laboratory (LLNL), Los Alamos National Laboratory, or Sandia National Laboratories, but also addresses the needs of users working in the unclassified environment. The Cielo Computational Environment Usage Model maps the provided capabilities to the tri-Lab ASC Computing Environment (ACE) Version 8.0 requirements. The ACE requirements reflect the high performance computing requirements for the Production Readiness Milestone user environment capabilities of the ASC community. A description of ACE requirements met, and those requirements that are not met, are included in each section of this document. The Cielo Computing Environment, along with the ACE mappings, has been issued and reviewed throughout the tri-Lab community.

Alternative Splicing Studies of the Reactive Oxygen Species Gene Network in Populus Reveal Two Isoforms of High-Isoelectric-Point Superoxide Dismutase1[C][W

Science.gov (United States)

Srivastava, Vaibhav; Srivastava, Manoj Kumar; Chibani, Kamel; Nilsson, Robert; Rouhier, Nicolas; Melzer, Michael; Wingsle, Gunnar

2009-01-01

Recent evidence has shown that alternative splicing (AS) is widely involved in the regulation of gene expression, substantially extending the diversity of numerous proteins. In this study, a subset of expressed sequence tags representing members of the reactive oxygen species gene network was selected from the PopulusDB database to investigate AS mechanisms in Populus. Examples of all known types of AS were detected, but intron retention was the most common. Interestingly, the closest Arabidopsis (Arabidopsis thaliana) homologs of half of the AS genes identified in Populus are not reportedly alternatively spliced. Two genes encoding the protein of most interest in our study (high-isoelectric-point superoxide dismutase [hipI-SOD]) have been found in black cottonwood (Populus trichocarpa), designated PthipI-SODC1 and PthipI-SODC2. Analysis of the expressed sequence tag libraries has indicated the presence of two transcripts of PthipI-SODC1 (hipI-SODC1b and hipI-SODC1s). Alignment of these sequences with the PthipI-SODC1 gene showed that hipI-SODC1b was 69 bp longer than hipI-SODC1s due to an AS event involving the use of an alternative donor splice site in the sixth intron. Transcript analysis showed that the splice variant hipI-SODC1b was differentially expressed, being clearly expressed in cambial and xylem, but not phloem, regions. In addition, immunolocalization and mass spectrometric data confirmed the presence of hipI-SOD proteins in vascular tissue. The functionalities of the spliced gene products were assessed by expressing recombinant hipI-SOD proteins and in vitro SOD activity assays. PMID:19176719

Usage of the cyclotron facility local area network

International Nuclear Information System (INIS)

Heinzmann, H.; Peters, J.; Thow, T.J.

1988-01-01

Local area network of controllers at the Karlsruhe cyclotyron is shown. Experience after two years of usage is described. The system is applied controlling, data acquisition, management, databases usage

Role of NPR1 dependent and NPR1 independent genes in response to Salicylic acid

Directory of Open Access Journals (Sweden)

Neha Agarwal

2017-10-01

Full Text Available NPR1 (Nonexpressor of pathogenesis-related gene is a transcription coactivator and central regulator of systemic acquired resistance (SAR pathway. It controls wide range of pathogenesis related genes involved in various defense responses, acts by sensing SAR signal molecule, Salicylic acid (SA. Mutation in NPR1 results in increased susceptibility to pathogen infection and less expression of pathogenesis related genes. The present study aimed to identify the role of NPR1 in gene expression after the Salicylic acid induction. For this RNA-seq was performed in Arabidopsis thaliana Col-0 and npr1-1 in response to Salicylic acid. RNA-seq analysis revealed a total of 3811 differentially expressed gene in which 2109 genes are up-regulated and 1702 genes are down-regulated. We have divided these genes in 6 categories SA induced (SI, SA repressed (SR, NPR1 dependent SI (ND-SI, NPR1 dependent SR (ND-SR, NPR1 independent SI (NI-SI, NPR1 independent SR (NI-SR. Further, Gene ontology and MapMan pathway analysis of differentially expressed genes suggested variety of biological processes and metabolic pathways that are enriched during SAR defense pathway. These results contribute to shed light on importance of both NPR1-dependent (ND and NPR1-independent (NI gene acting downstream to Salicylic acid induction in SAR pathway. The present study aimed to identify the role of NPR1 in gene expression after the Salicylic acid induction.

Studies of Neurofibromatosis-1 Modifier Genes

Science.gov (United States)

2005-06-01

characterize patients of the FANCD1 complementation group (Howlett et al., 2002), and FANCA , which is the most frequently mutated FA gene , maps to a 650 kb...associations, we genotyped a total of 16 SNPs in FANCA and three immediately adjacent genes and collaborated with statistical geneticist Dr. Mark Daly at MIT to...across 15 SNPs in FANCA and the adjacent FLJ12547, CDKIO, and SPG7 genes . Red/pink coloration indicates statistical significance (LOD=3). The number in

The conserved Lysine69 residue plays a catalytic role in Mycobacterium tuberculosis shikimate dehydrogenase

Directory of Open Access Journals (Sweden)

Rodrigues Valnês

2009-01-01

Full Text Available Abstract Background The shikimate pathway is an attractive target for the development of antitubercular agents because it is essential in Mycobacterium tuberculosis, the causative agent of tuberculosis, but absent in humans. M. tuberculosis aroE-encoded shikimate dehydrogenase catalyzes the forth reaction in the shikimate pathway. Structural and functional studies indicate that Lysine69 may be involved in catalysis and/or substrate binding in M. tuberculosis shikimate dehydrogenase. Investigation of the kinetic properties of mutant enzymes can bring important insights about the role of amino acid residues for M. tuberculosis shikimate dehydrogenase. Findings We have performed site-directed mutagenesis, steady-state kinetics, equilibrium binding measurements and molecular modeling for both the wild-type M. tuberculosis shikimate dehydrogenase and the K69A mutant enzymes. The apparent steady-state kinetic parameters for the M. tuberculosis shikimate dehydrogenase were determined; the catalytic constant value for the wild-type enzyme (50 s-1 is 68-fold larger than that for the mutant K69A (0.73 s-1. There was a modest increase in the Michaelis-Menten constant for DHS (K69A = 76 μM; wild-type = 29 μM and NADPH (K69A = 30 μM; wild-type = 11 μM. The equilibrium dissociation constants for wild-type and K69A mutant enzymes are 32 (± 4 μM and 134 (± 21, respectively. Conclusion Our results show that the residue Lysine69 plays a catalytic role and is not involved in substrate binding for the M. tuberculosis shikimate dehydrogenase. These efforts on M. tuberculosis shikimate dehydrogenase catalytic mechanism determination should help the rational design of specific inhibitors, aiming at the development of antitubercular drugs.

Antibody repertoires in humanized NOD-scid-IL2Rγ(null mice and human B cells reveals human-like diversification and tolerance checkpoints in the mouse.

Directory of Open Access Journals (Sweden)

Gregory C Ippolito

Full Text Available Immunodeficient mice reconstituted with human hematopoietic stem cells enable the in vivo study of human hematopoiesis. In particular, NOD-scid-IL2Rγ(null engrafted mice have been shown to have reasonable levels of T and B cell repopulation and can mount T-cell dependent responses; however, antigen-specific B-cell responses in this model are generally poor. We explored whether developmental defects in the immunoglobulin gene repertoire might be partly responsible for the low level of antibody responses in this model. Roche 454 sequencing was used to obtain over 685,000 reads from cDNA encoding immunoglobulin heavy (IGH and light (IGK and IGL genes isolated from immature, naïve, or total splenic B cells in engrafted NOD-scid-IL2Rγ(null mice, and compared with over 940,000 reads from peripheral B cells of two healthy volunteers. We find that while naïve B-cell repertoires in humanized mice are chiefly indistinguishable from those in human blood B cells, and display highly correlated patterns of immunoglobulin gene segment use, the complementarity-determining region H3 (CDR-H3 repertoires are nevertheless extremely diverse and are specific for each individual. Despite this diversity, preferential D(H-J(H pairings repeatedly occur within the CDR-H3 interval that are strikingly similar across all repertoires examined, implying a genetic constraint imposed on repertoire generation. Moreover, CDR-H3 length, charged amino-acid content, and hydropathy are indistinguishable between humans and humanized mice, with no evidence of global autoimmune signatures. Importantly, however, a statistically greater usage of the inherently autoreactive IGHV4-34 and IGKV4-1 genes was observed in the newly formed immature B cells relative to naïve B or total splenic B cells in the humanized mice, a finding consistent with the deletion of autoreactive B cells in humans. Overall, our results provide evidence that key features of the primary repertoire are shaped by

Identification of Phosphoglycerate Kinase 1 (PGK1 as a reference gene for quantitative gene expression measurements in human blood RNA

Directory of Open Access Journals (Sweden)

Unger Elizabeth R

2011-09-01

Full Text Available Abstract Background Blood is a convenient sample and increasingly used for quantitative gene expression measurements with a variety of diseases including chronic fatigue syndrome (CFS. Quantitative gene expression measurements require normalization of target genes to reference genes that are stable and independent from variables being tested in the experiment. Because there are no genes that are useful for all situations, reference gene selection is an essential step to any quantitative reverse transcription-PCR protocol. Many publications have described appropriate genes for a wide variety of tissues and experimental conditions, however, reference genes that may be suitable for the analysis of CFS, or human blood RNA derived from whole blood as well as isolated peripheral blood mononuclear cells (PBMCs, have not been described. Findings Literature review and analyses of our unpublished microarray data were used to narrow down the pool of candidate reference genes to six. We assayed whole blood RNA from Tempus tubes and cell preparation tube (CPT-collected PBMC RNA from 46 subjects, and used the geNorm and NormFinder algorithms to select the most stable reference genes. Phosphoglycerate kinase 1 (PGK1 was one of the optimal normalization genes for both whole blood and PBMC RNA, however, additional genes differed for the two sample types; Ribosomal protein large, P0 (RPLP0 for PBMC RNA and Peptidylprolyl isomerase B (PPIB for whole blood RNA. We also show that the use of a single reference gene is sufficient for normalization when the most stable candidates are used. Conclusions We have identified PGK1 as a stable reference gene for use with whole blood RNA and RNA derived from PBMC. When stable genes are selected it is possible to use a single gene for normalization rather than two or three. Optimal normalization will improve the ability of results from PBMC RNA to be compared with those from whole blood RNA and potentially allows comparison of

textbf{Historical Usage Inventories of DDT in China}

Science.gov (United States)

Qiang, Wang; Lijuan, Zhao; Jianxin, Hu

2010-05-01

from dicofol use and 766 tons applied for malaria control, and the annual average usage of DDT was 766 tons. Spatial distribution of DDT usage has direct relationship with sown areas of cotton, apple, citrus, tea and vegetable, and the DDT usage is concentrated in middle and east China where there is large sown area of cotton and apple, the historical use trend is affected by the weather and acarid harm. On province scale in China, Shandong province was the largest consumer of DDT, whose usage added up to 2,094 tons. On prefecture scale, Xianyang city was the largest consumer of DDT, adding up to 304 tons. Shandong province used the most of DDT resulting from dicofol among the provinces/regions, adding up to 1,866 tons; and Yunnan Province used the most of DDT applied for malaria control among the prefectures, adding up to 481 tons.

Flagellar-phase variation: isolation of the rh1 gene

International Nuclear Information System (INIS)

Silverman, M.; Zieg, J.; Simon, M.

1979-01-01

In Salmonella, expression of flagellar antigen alternates between two serotypes (phases) encoded by two genes, H1 and H2. The mechanism which controls the alternative expression of the H1 and H2 genes was examined by cloning these genes and the genetic elements which control their activity on hybrid vehicles in Escherichia coli. H2 gene activity was shown to be controlled by a recombinational switch located adjacent to the H2 gene. Activity of the H1 gene is thought to be repressed, when the H2 gene is expressed, by the product of another gene, rhl (repressor of H1), which is controlled coordinately with the H2 gene. In this report, we describe the construction of hybrid lambda vehicles which contain, in addition to the H2 gene, a genetic activity corresponding to rhl. Variation of flagellar antigens analogous to that observed in Salmonella was observed when E. coli strains were transduced with the hybrid lambda. By using the lambda H2rhl hybrid to program protein syntheis in uv-irradiated cells, the synthesis of a polypeptide was correlated with rhl gene product activity. We conclude that the H2 region consists of two cotranscribed genes, H2 and rhl. The expression of both gene products is regulated by the same recombinational event

In Silico Analysis of FMR1 Gene Missense SNPs.

Science.gov (United States)

Tekcan, Akin

2016-06-01

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

Gene number determination and genetic polymorphism of the gamma delta T cell co-receptor WC1 genes

Directory of Open Access Journals (Sweden)

Chen Chuang

2012-10-01

Full Text Available Abstract Background WC1 co-receptors belong to the scavenger receptor cysteine-rich (SRCR superfamily and are encoded by a multi-gene family. Expression of particular WC1 genes defines functional subpopulations of WC1+ γδ T cells. We have previously identified partial or complete genomic sequences for thirteen different WC1 genes through annotation of the bovine genome Btau_3.1 build. We also identified two WC1 cDNA sequences from other cattle that did not correspond to sequences in the Btau_3.1 build. Their absence in the Btau_3.1 build may have reflected gaps in the genome assembly or polymorphisms among animals. Since the response of γδ T cells to bacterial challenge is determined by WC1 gene expression, it was critical to understand whether individual cattle or breeds differ in the number of WC1 genes or display polymorphisms. Results Real-time quantitative PCR using DNA from the animal whose genome was sequenced (“Dominette” and sixteen other animals representing ten breeds of cattle, showed that the number of genes coding for WC1 co-receptors is thirteen. The complete coding sequences of those thirteen WC1 genes is presented, including the correction of an error in the WC1-2 gene due to mis-assembly in the Btau_3.1 build. All other cDNA sequences were found to agree with the previous annotation of complete or partial WC1 genes. PCR amplification and sequencing of the most variable N-terminal SRCR domain (domain 1 which has the SRCR “a” pattern of each of the thirteen WC1 genes showed that the sequences are highly conserved among individuals and breeds. Of 160 sequences of domain 1 from three breeds of cattle, no additional sequences beyond the thirteen described WC1 genes were found. Analysis of the complete WC1 cDNA sequences indicated that the thirteen WC1 genes code for three distinct WC1 molecular forms. Conclusion The bovine WC1 multi-gene family is composed of thirteen genes coding for three structural forms whose

Determination of Toll-Like Receptor 1 Gene Polymorphisms in Zavot, Turkish Grey, East Anatolian Red, Anatolian Black and South Anatolian Red Cattle Breeds

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Mehmet Ulaş Çınar

2016-05-01

Full Text Available Toll-like receptors (TLRs play an important role in non-specific immunity against different infectious agents such as bacterium or parasite. The aim of this work was to investigate the allele and genotype frequencies of three single-nucleotide polymorphisms (SNPs in bovine TLR1 gene in native Turkish cattle breeds. DNA samples were extracted using the phenol chloroform protocol from 77 Zavot, 60 Turkish Grey, 51 East Anatolian Red, 69 Anatolian Black and 46 South Anatolian Red cattle. Target regions of the TLR1 gene were digested BsII and HpyI88III restriction enzymes. Results showed that the (A allele frequency had higher in all native Turkish cattle breeds of the TLR1-G1409A locus. The (F allele frequency was found to be higher compared to (E allele in the TLR1-G1550A site. The frequencies of both (C and (T alleles were close to each other in the TLR1-C632T site. In conclusion genetic polymorphisms exist in Turkish native cattle populations in terms of known TLR1 variants.

Nomenclature for alleles of the human carboxylesterase 1 gene

DEFF Research Database (Denmark)

Rasmussen, Henrik B.; Madsen, Majbritt B.; Bjerre, Ditte

2017-01-01

The carboxylesterase 1 gene (CES1) in humans encodes a hydrolase, which is implicated in the metabolism of several commonly used drugs 1. This gene is located on chromosome 16 with a highly homologous pseudogene, CES1P1, in its proximity. A duplicated segment of CES1 replaces most of CES1P1 in some...... appears to be low 8,13. The formation of hybrids consisting of a gene and a related pseudogene has been reported for other genes than CES1. This includes the hybrids of the gene encoding cytochrome P450 2D6 (CYP2D6) and pseudogene CYP2D7, that is, the so-called CYP2D7/D6 hybrids 14......,15. These are categorized as CYP2D6 variants and not as variants of pseudogene CYP2D716....

Review of Bison Usage in VERA

Energy Technology Data Exchange (ETDEWEB)

Gardner, Russell [Idaho National Lab. (INL), Idaho Falls, ID (United States); Pawlowski, Roger P. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Clarno, Kevin T. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Stimpson, Shane G. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

2017-11-01

Bison is being used in VERA in a variety of ways; this milestone will document an independent review of the current usage of Bison and provide guidance that will improve the accuracy, performance, and consistency in the ways that Bison is used. This task will entail running a suite of small, single and multi-cycle problems with VERA-CS, followed by Bison, and Tiamat (inline) and evaluating the usage. It will also entail performing several detailed ramp to full power solutions to compare the one-way coupled solver with the fully-coupled Tiamat. This will include at least one iteration with the PHI team to incorporate some of the feedback and improve the usage. This work will also be completed in conjunction with an FMC task to evaluate the ability of Bison to model load-follow in a PWR

Impact of AtNHX1, a vacuolar Na+/H+ antiporter, upon gene expression during short- and long-term salt stress in Arabidopsis thaliana

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Blumwald Eduardo

2007-04-01

Full Text Available Abstract Background AtNHX1, the most abundant vacuolar Na+/H+ antiporter in Arabidopsis thaliana, mediates the transport of Na+ and K+ into the vacuole, influencing plant development and contributing to salt tolerance. In this report, microarray expression profiles of wild type plants, a T-DNA insertion knockout mutant of AtNHX1 (nhx1, and a 'rescued' line (NHX1::nhx1 were exposed to both short (12 h and 48 h and long (one and two weeks durations of a non-lethal salt stress to identify key gene transcripts associated with the salt response that are influenced by AtNHX1. Results 147 transcripts showed both salt responsiveness and a significant influence of AtNHX1. Fifty-seven of these genes showed an influence of the antiporter across all salt treatments, while the remaining genes were influenced as a result of a particular duration of salt stress. Most (69% of the genes were up-regulated in the absence of AtNHX1, with the exception of transcripts encoding proteins involved with metabolic and energy processes that were mostly down-regulated. Conclusion While part of the AtNHX1-influenced transcripts were unclassified, other transcripts with known or putative roles showed the importance of AtNHX1 to key cellular processes that were not necessarily limited to the salt stress response; namely calcium signaling, sulfur metabolism, cell structure and cell growth, as well as vesicular trafficking and protein processing. Only a small number of other salt-responsive membrane transporter transcripts appeared significantly influenced by AtNHX1.

Joint pain epidemiology and analgesic usage in Madagascar.

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Samison, Luc Hervé; Randriatsarafara, Fidiniaina Mamy; Ralandison, Stéphane

2017-01-01

To describe the epidemiology of joint pains and document analgesics usage in an African context. Patients suffering from joint pain were recruited from nine sites located in Antananarivo, Madagascar, including 6 hospital services and 3 clinics. Doctors collected information on the etiology and characteristics of the patients' pain. Analgesics prescribed by these doctors were also documented. In total, 400 patients were enrolled in the study (52.5% women, mean age of 42.34 years ± 17.7 [4-86]). Pain of mechanical type was found in 260 participants, 65%; 95% CI [60.1% to 69.6%] and inflammatory type pains in 128 cases 32%; 95% CI [27.5% to 36.9%]. Mixed pains were found in 12 patients (3%). The median duration of pain prior to the consultation was 6.5 days. The average pain intensity was 57.9 ± 19.9 mm of a total of 100 mm maximum on a visual analogue scale, VAS. The etiologies of mechanical type pains were dominated by fracture, common low back pain and tendonitis. Arthrosis was the dominant cause of inflammatory type pain, followed by rheumatoid arthritis and gout. NSAIDs (74.5%) were the most frequently prescribed analgesics followed by paracetamol (49.5%), weak opioids (23%) and corticosteroids (12.25%). Two-thirds of medical prescriptions (65.3%) were of combined analgesics. These findings demonstrated that mechanical type pains were the main reason for consultations for joint pain in these situations in Antananarivo, Madagascar. The most frequently prescribed pain-relieving medications were NSAIDs, paracetamol, weak opioids and corticosteroids. This descriptive study may be a useful starting point for further epidemiological studies of pain in the African context.

Inflammatory Gene Polymorphisms in Lung Cancer Susceptibility.

Science.gov (United States)

Eaton, Keith D; Romine, Perrin E; Goodman, Gary E; Thornquist, Mark D; Barnett, Matt J; Petersdorf, Effie W

2018-05-01

Chronic inflammation has been implicated in carcinogenesis, with increasing evidence of its role in lung cancer. We aimed to evaluate the role of genetic polymorphisms in inflammation-related genes in the risk for development of lung cancer. A nested case-control study design was used, and 625 cases and 625 well-matched controls were selected from participants in the β-Carotene and Retinol Efficacy Trial, which is a large, prospective lung cancer chemoprevention trial. The association between lung cancer incidence and survival and 23 polymorphisms descriptive of 11 inflammation-related genes (interferon gamma gene [IFNG], interleukin 10 gene [IL10], interleukin 1 alpha gene [IL1A], interleukin 1 beta gene [IL1B], interleukin 2 gene [IL2], interleukin 4 receptor gene [IL4R], interleukin 4 gene [IL4], interleukin 6 gene [IL6], prostaglandin-endoperoxide synthase 2 gene [PTGS2] (also known as COX2), transforming growth factor beta 1 gene [TGFB1], and tumor necrosis factor alpha gene [TNFA]) was evaluated. Of the 23 polymorphisms, two were associated with risk for lung cancer. Compared with individuals with the wild-type (CC) variant, individuals carrying the minor allele variants of the IL-1β-511C>T promoter polymorphism (rs16944) (CT and TT) had decreased odds of lung cancer (OR = 0.74, [95% confidence interval (CI): 0.58-0.94] and OR = 0.71 [95% CI: 0.50-1.01], respectively, p = 0.03). Similar results were observed for the IL-1β-1464 C>G promoter polymorphism (rs1143623), with presence of the minor variants CG and CC having decreased odds of lung cancer (OR = 0.75 [95% CI: 0.59-0.95] and OR = 0.69 [95% CI: 0.46-1.03], respectively, p = 0.03). Survival was not influenced by genotype. This study provides further evidence that IL1B promoter polymorphisms may modulate the risk for development of lung cancer. Copyright © 2018 International Association for the Study of Lung Cancer. Published by Elsevier Inc. All rights reserved.

Overview of recent developments in chronic lymphocytic leukemia

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Preetesh Jain

2012-01-01

Full Text Available Multiple advances have been made in our understanding of pathobiology of chronic lymphocytic leukemia (CLL. These developments in the laboratory include new prognostic markers, risk stratification of the disease and newer therapeutic agents in CLL. These advances in CLL have come a long way in the past three decades since the development of Rai and Binet clinical staging systems. Important strides in the pathobiology, from defining mutational status of IGHV, to B-cell receptor (BCR signaling pathways and CLL microenvironment have made a major difference in our understanding of this disease. Mutational status of immunoglobulin heavy chain genes (IGHV, CD38 and Zap-70, chromosomal aberrations and newer mutations, are the most clinically relevant prognostic markers. Chemoimmunotherapy (CIT has become the treatment of choice for young and fit CLL patients. Various inhibitors of BCR signaling pathways and immunomodulatory drugs have shown efficacy in clinical trials. The most recent advance is the use of chimeric antigen receptor therapy (CAR based on autologous T-lymphocytes. Nevertheless, CLL remains an incurable disease today. Coordinated developments between laboratory and clinic will hopefully translate into a cure for CLL. This short review focuses on advances in prognostication and therapy in CLL.

Students' access usage and awareness of electronic information ...

African Journals Online (AJOL)

Students' access usage and awareness of electronic information resources at the University College Hospital, University of Ibadan, Nigeria. RA Ojo, SO Akande. Abstract. No Abstract. Lagos Journal of Library and Information Science Vol. 3(1) 2005: 16-24. Full Text: EMAIL FULL TEXT EMAIL FULL TEXT · DOWNLOAD ...

Health-related behaviors and technology usage among college students.

Science.gov (United States)

Melton, Bridget F; Bigham, Lauren E; Bland, Helen W; Bird, Matthew; Fairman, Ciaran

2014-07-01

To examine associations between technology usage and specific health factors among college students. The research employed was a quantitative, descriptive, cross-sectional design; undergraduate students enrolled in spring 2012 general health education courses were recruited to participate. To explore college students' specific technology usage and health-related behaviors, a 28-item questionnaire was utilized. Statistical significant differences of technology usage were found between 3 of the 4 health-related behaviors under study (BMI, sleep, and nutrition) (p technology usage continues to evolve within the college student population, health professionals need to understand its implications on health behaviors.

Association of Cytochrome CYP1A1 Gene Polymorphisms and Tobacco Smoking With the Risk of Breast Cancer in Women From Iraq

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Hassan M. Naif

2018-04-01

Full Text Available BackgroundCYP1A1 gene polymorphisms and tobacco smoking are among several risk factors for various types of cancers, but their influence on breast cancer remains controversial. We analyzed the possible association of CYP1A1 gene polymorphisms and tobacco smoking-related breast cancer in women from Iraq.Materials and methodsIn this case–control study, gene polymorphism of CYP1A1 gene (CYP1A1m1, T6235C and CYP1A1m2, A4889G of 199 histologically verified breast cancer patients’ and 160 cancer-free control women’s specimens were performed by using PCR-based restriction fragment length polymorphism.ResultsThree genotype frequencies (TT, TC, and CC of CYP1A1m1T/C appeared in 16.1, 29.6, and 54.3% of women with breast cancer, respectively, compared with 41.2, 40, and 18.8% in the control group, respectively. CYP1A1m1 CC genotype and C allele were significantly associated with increased risks for breast cancer in patients (54.3 and 69%, respectively compared with controls (18.8 and 39%, respectively. While the three genotype frequencies (AA, AG, and GG of CYP1A1m2A/G were detected in 20.1, 31.2, and 48.7% in patients compared with 46.3, 40.6, and 13.1% in controls, respectively. The frequency of GG genotypes and G allele was significantly higher in patients (48.7 and 64%, respectively than in the controls (13.1 and 33%, respectively. Smoking women having either CC or GG genotypes showed a highly significant association with increased risk of breast cancer [odds ratio (OR = 1.607, 95% confidence interval (CI 0.91–1.64, p = 0.0001, and OR, 1.841, 95% CI, 0.88–1.67, p = 0.0001, respectively]. On the other hand, the T and A alleles of predominantly seen in healthy smoking women (83 and 85%, p = 0.0001, respectively.ConclusionThese findings indicated that both C and G alleles of CYP1A1m1 and m2 were significantly associated with elevated risk of breast cancer in Iraqi women, while the T and A alleles were predominantly seen in

Informing Evidence Based Decisions: Usage Statistics for Online Journal Databases

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Alexei Botchkarev

2017-06-01

Full Text Available Abstract Objective – The primary objective was to examine online journal database usage statistics for a provincial ministry of health in the context of evidence based decision-making. In addition, the study highlights implementation of the Journal Access Centre (JAC that is housed and powered by the Ontario Ministry of Health and Long-Term Care (MOHLTC to inform health systems policy-making. Methods – This was a prospective case study using descriptive analysis of the JAC usage statistics of journal articles from January 2009 to September 2013. Results – JAC enables ministry employees to access approximately 12,000 journals with full-text articles. JAC usage statistics for the 2011-2012 calendar years demonstrate a steady level of activity in terms of searches, with monthly averages of 5,129. In 2009-2013, a total of 4,759 journal titles were accessed including 1,675 journals with full-text. Usage statistics demonstrate that the actual consumption was over 12,790 full-text downloaded articles or approximately 2,700 articles annually. Conclusion – JAC’s steady level of activities, revealed by the study, reflects continuous demand for JAC services and products. It testifies that access to online journal databases has become part of routine government knowledge management processes. MOHLTC’s broad area of responsibilities with dynamically changing priorities translates into the diverse information needs of its employees and a large set of required journals. Usage statistics indicate that MOHLTC information needs cannot be mapped to a reasonably compact set of “core” journals with a subsequent subscription to those.

Learning disabilities: analysis of 69 children

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Meister Eduardo Kaehler

2001-01-01

Full Text Available With this article we intend to demonstrate the importance of evaluation and follow up of children with learning disabilities, through a multidisciplinary team. As well as to establish the need of intervention. We evaluate 69 children, from Aline Picheth Public School, in Curitiba, attending first or second grade of elementary school, through general and evolutionary neurological examination, pediatric checklist symptoms, and social, linguistic and psychological (WISC-III, Bender Infantile and WPPSI-figures evaluation. The incidence was higher in boys (84,1%, familiar history of learning disabilities was found in 42%, and writing abnormalities in 56,5%. The most frequent diagnosis was attention deficit and hyperactivity disorder, in 39,1%. With this program, we aimed to reduce the retention taxes and stress the importance of this evaluation, and, if necessary, multidisciplinar intervention in the cases of learning disabilities.

Gene program-specific regulation of PGC-1{alpha} activity

DEFF Research Database (Denmark)

Schmidt, Søren F; Mandrup, Susanne

2011-01-01

Peroxisome proliferator-activated receptor γ (PPARγ) coactivator 1 α (PGC-1α) activation coordinates induction of the hepatic fasting response through coactivation of numerous transcription factors and gene programs. In the June 15, 2011, issue of Genes & Development, Lustig and colleagues (pp....... 1232-1244) demonstrated that phosphorylation of PGC-1α by the p70 ribosomal protein S6 kinase 1 (S6K1) specifically interfered with the interaction between PGC-1α and HNF4α in liver and blocked the coactivation of the gluconeogenic target genes. This demonstrates how independent fine-tuning of gene...

Measurement of the np total cross section difference Δ σ L(np) at 1.39, 1.69, 1.89 and 1.99 GeV

Science.gov (United States)

Sharov, V. I.; Anischenko, N. G.; Antonenko, V. G.; Averichev, S. A.; Azhgirey, L. S.; Bartenev, V. D.; Bazhanov, N. A.; Belyaev, A. A.; Blinov, N. A.; Borisov, N. S.; Borzakov, S. B.; Borzunov, Yu T.; Bushuev, Yu P.; Chernenko, L. P.; Chernykh, E. V.; Chumakov, V. F.; Dolgii, S. A.; Fedorov, A. N.; Fimushkin, V. V.; Finger, M.; Finger, M.; Golovanov, L. B.; Gurevich, G. M.; Janata, A.; Kirillov, A. D.; Kolomiets, V. G.; Komogorov, E. V.; Kovalenko, A. D.; Kovalev, A. I.; Krasnov, V. A.; Krstonoshich, P.; Kuzmin, E. S.; Ladygin, V. P.; Lazarev, A. B.; Lehar, F.; de Lesquen, A.; Liburg, M. Yu; Livanov, A. N.; Lukhanin, A. A.; Maniakov, P. K.; Matafonov, V. N.; Matyushevsky, E. A.; Moroz, V. D.; Morozov, A. A.; Neganov, A. B.; Nikolaevsky, G. P.; Nomofilov, A. A.; Panteleev, Tz; Pilipenko, Yu K.; Pisarev, I. L.; Plis, Yu A.; Polunin, Yu P.; Prokofiev, A. N.; Prytkov, V. Yu; Rukoyatkin, P. A.; Schedrov, V. A.; Schevelev, O. N.; Shilov, S. N.; Shindin, R. A.; Slunečka, M.; Slunečková, V.; Starikov, A. Yu; Stoletov, G. D.; Strunov, L. N.; Svetov, A. L.; Usov, Yu A.; Vasiliev, T.; Volkov, V. I.; Vorobiev, E. I.; Yudin, I. P.; Zaitsev, I. V.; Zhdanov, A. A.; Zhmyrov, V. N.

2004-09-01

New accurate results of the neutron-proton spin-dependent total cross section difference Δσ_L(np) at the neutron beam kinetic energies 1.39, 1.69, 1.89 and 1.99 GeV are presented. Measurements were carried out in 2001 at the Synchrophasotron of the Veksler and Baldin Laboratory of High Energies of the Joint Institute for Nuclear Research. A quasi-monochromatic neutron beam was produced by break-up of extracted polarized deuterons. The deuteron (and hence neutron) polarization direction was flipped every accelerator burst. The vertical neutron polarization direction was rotated onto the neutron beam direction and longitudinally (L) polarized neutrons were transmitted through a large proton L-polarized target. The target polarization vector was inverted after 1-2 days of measurements. The data were recorded for four different combinations of the beam and target parallel and antiparallel polarization directions at each energy. A fast decrease of Δσ_L(np) with increasing energy above 1.1 GeV was confirmed. The structure in the Δσ_L(np) energy dependence around 1.8 GeV, first observed from our previous data, seems to be well pronounced. The new results are also compared with model predictions and with phase shift analysis fits. The Δσ_L quantities for isosinglet state I = 0, deduced from the measured Δσ_L(np) values and the known Δσ_L(pp) data, are also given. The results were completed by the measurements of unpolarized total cross sections σ_{0tot}(np) at 1.3, 1.4 and 1.5 GeV and σ_{0tot}(nC) at 1.4 and 1.5 GeV. These data were obtained using the same apparatus and high intensity unpolarized deuteron beams were extracted either from the Synchrophasotron, or from the Nuclotron.

Gene prediction validation and functional analysis of redundant pathways

DEFF Research Database (Denmark)

Sønderkær, Mads

2011-01-01

have employed a large mRNA-seq data set to improve and validate ab initio predicted gene models. This direct experimental evidence also provides reliable determinations of UTR regions and polyadenylation sites, which are not easily predicted in plants. Furthermore, once an annotated genome sequence...... is available, gene expression by mRNA-Seq enables acquisition of a more complete overview of gene isoform usage in complex enzymatic pathways enabling the identification of key genes. Metabolism in potatoes This information is useful e.g. for crop improvement based on manipulation of agronomically important...

Usage rate segmentation: enriching the US wine market profile

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Kelley K

2015-05-01

Full Text Available Kathleen Kelley,1 Jeffrey Hyde,2 Johan Bruwer3 1Department of Plant Science, 2Department of Agricultural Economics, Sociology, and Education, The Pennsylvania State University, University Park, PA, USA; 3School of Marketing, University of South Australia, Adelaide, SA, Australia Abstract: The purpose of this research is to enrich our knowledge of the US wine market and provide insights into how usage rate segmentation can be enhanced by select innovative perspectives of current offerings. Data were collected through a 15-minute online survey of 910 US wine drinkers randomly selected from a panel of consumers. It was found that the “super core” segment not only drank wine more frequently, but also were more likely to drink other types of alcohol presented (beer, distilled spirits, and ready-to-drink cocktails, and at a greater frequency, “at least once a week” and “about once a week”, than “marginal” drinkers. Differences between usage rate segments existed between sex and age generations. Female millennial “super core” consumers would increase wine consumption if the number of calories were reduced to fewer than 80 per 5 oz serving. Practical implications for a winery or wine retailer might include the potential to add these beverages to their product offering or bundling these beverages to create packages (allowing for mass customization, which is used often in retail and appropriately marketing these offerings to their customers. Changes that may invoke a positive response are wine made from “sustainably farmed” or “naturally farmed” grapes, and certified carbon-free wine. From an originality viewpoint, this study is the first to investigate how usage rate segmentation can be enriched by means of variable cross-extension and examination. Keywords: consumer behavior, market segmentation, usage rate, consumption frequency, USA

A Hybrid Data Mining Approach for Credit Card Usage Behavior Analysis

Science.gov (United States)

Tsai, Chieh-Yuan

Credit card is one of the most popular e-payment approaches in current online e-commerce. To consolidate valuable customers, card issuers invest a lot of money to maintain good relationship with their customers. Although several efforts have been done in studying card usage motivation, few researches emphasize on credit card usage behavior analysis when time periods change from t to t+1. To address this issue, an integrated data mining approach is proposed in this paper. First, the customer profile and their transaction data at time period t are retrieved from databases. Second, a LabelSOM neural network groups customers into segments and identify critical characteristics for each group. Third, a fuzzy decision tree algorithm is used to construct usage behavior rules of interesting customer groups. Finally, these rules are used to analysis the behavior changes between time periods t and t+1. An implementation case using a practical credit card database provided by a commercial bank in Taiwan is illustrated to show the benefits of the proposed framework.

47 CFR 69.303 - Information origination/termination equipment (IOT).

Science.gov (United States)

2010-10-01

... 47 Telecommunication 3 2010-10-01 2010-10-01 false Information origination/termination equipment (IOT). 69.303 Section 69.303 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON... origination/termination equipment (IOT). Investment in all other IOT shall be apportioned between the Special...

Usage of DNA Fingerprinting Technology for Quality Control in Molecular Lab Bench Work.

Science.gov (United States)

McIntosh, Linda Y; Lal, Janella E; Qin, Dahui

2018-01-01

One of the major quality assurance (QA) goals in many molecular laboratories is to avoid sample pipetting errors on the lab bench; especially when pipetting into multiwell plates. A pipetting error can cause a switch in patient samples, which can lead to recording the wrong results for the patient samples involved. Such pipetting errors are difficult to identify when it happens in lab bench work. DNA fingerprinting is a powerful tool in determining sample identities. Our laboratory has explored the usage of this technology in our QA process and successfully established that DNA fingerprinting can be used to monitor possible sample switch in gene rearrangement lab bench work. We use florescent light to quench the florescence in the gene rearrangement polymerase chain reaction products. After that, DNA fingerprinting technology is used to identify the sample DNA in the gene rearrangement polymerase chain reaction plate. The result is compared with the corresponding patient's blood sample DNA to determine whether there is a sample switch during the lab bench work.

The Role of a Novel TRMT1 Gene Mutation and Rare GRM1 Gene Defect in Intellectual Disability in Two Azeri Families.

Science.gov (United States)

Davarniya, Behzad; Hu, Hao; Kahrizi, Kimia; Musante, Luciana; Fattahi, Zohreh; Hosseini, Masoumeh; Maqsoud, Fariba; Farajollahi, Reza; Wienker, Thomas F; Ropers, H Hilger; Najmabadi, Hossein

2015-01-01

Cognitive impairment or intellectual disability (ID) is a widespread neurodevelopmental disorder characterized by low IQ (below 70). ID is genetically heterogeneous and is estimated to affect 1-3% of the world's population. In affected children from consanguineous families, autosomal recessive inheritance is common, and identifying the underlying genetic cause is an important issue in clinical genetics. In the framework of a larger project, aimed at identifying candidate genes for autosomal recessive intellectual disorder (ARID), we recently carried out single nucleotide polymorphism-based genome-wide linkage analysis in several families from Ardabil province in Iran. The identification of homozygosity-by-descent loci in these families, in combination with whole exome sequencing, led us to identify possible causative homozygous changes in two families. In the first family, a missense variant was found in GRM1 gene, while in the second family, a frameshift alteration was identified in TRMT1, both of which were found to co-segregate with the disease. GRM1, a known causal gene for autosomal recessive spinocerebellar ataxia (SCAR13, MIM#614831), encodes the metabotropic glutamate receptor1 (mGluR1). This gene plays an important role in synaptic plasticity and cerebellar development. Conversely, the TRMT1 gene encodes a tRNA methyltransferase that dimethylates a single guanine residue at position 26 of most tRNAs using S-adenosyl methionine as the methyl group donor. We recently presented TRMT1 as a candidate gene for ARID in a consanguineous Iranian family (Najmabadi et al., 2011). We believe that this second Iranian family with a biallelic loss-of-function mutation in TRMT1 gene supports the idea that this gene likely has function in development of the disorder.

Definite Article Usage across Varieties of English

Science.gov (United States)

Wahid, Ridwan

2013-01-01

This paper seeks to explore the extent of definite article usage variation in several varieties of English based on a classification of its usage types. An annotation scheme based on Hawkins and Prince was developed for this purpose. Using matching corpus data representing Inner Circle varieties and Outer Circle varieties, analysis was made on…

Comparing usage of a web and app stress management intervention: An observational study

Directory of Open Access Journals (Sweden)

Leanne G. Morrison

2018-06-01

Full Text Available Choices in the design and delivery of digital health behaviour interventions may have a direct influence on subsequent usage and engagement. Few studies have been able to make direct, detailed comparisons of differences in usage between interventions that are delivered via web or app. This study compared the usage of two versions of a digital stress management intervention, one delivered via a website (Healthy Paths and the other delivered via an app (Healthy Mind. Design modifications were introduced within Healthy Mind to take account of reported differences in how individuals engage with websites compared to apps and mobile phones. Data were collected as part of an observational study nested within a broader exploratory trial of Healthy Mind. Objective usage of Healthy Paths and Healthy Mind were automatically recorded, including frequency and duration of logins, access to specific components within the intervention and order of page/screen visits. Usage was compared for a two week period following initial registration. In total, 381 participants completed the registration process for Healthy Paths (web and 162 participants completed the registration process for Healthy Mind (app. App users logged in twice as often (Mdn = 2.00 as web users (Mdn = 1.00, U = 13,059.50, p ≤ 0.001, but spent half as much time (Mdn = 5.23 min on the intervention compared to web users (Mdn = 10.52 min, U = 19,740.00, p ≤ 0.001. Visual exploration of usage patterns over time revealed that a significantly higher proportion of app users (n = 126, 82.35% accessed both types of support available within the intervention (i.e. awareness and change-focused tools compared to web users (n = 92, 40.17%, χ2(1, n = 382 = 66.60, p < 0.001. This study suggests that the digital platform used to deliver an intervention (i.e. web versus app and specific design choices (e.g. navigation, length and volume of content may be

Regional gene expression of LOX-1, VCAM-1, and ICAM-1 in aorta of HIV-1 transgenic rats.

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Anne Mette Fisker Hag

Full Text Available BACKGROUND: Increased prevalence of atherosclerotic cardiovascular disease in HIV-infected patients has been observed. The cause of this accelerated atherosclerosis is a matter of controversy. As clinical studies are complicated by a multiplicity of risk-factors and a low incidence of hard endpoints, studies in animal models could be attractive alternatives. METHODOLOGY/PRINCIPAL FINDINGS: We evaluated gene expression of lectin-like oxidized-low-density-lipoprotein receptor-1 (LOX-1, vascular cell adhesion molecule-1 (VCAM-1, and intercellular adhesion molecule-1 (ICAM-1 in HIV-1 transgenic (HIV-1Tg rats; these genes are all thought to play important roles in early atherogenesis. Furthermore, the plasma level of sICAM-1 was measured. We found that gene expressions of LOX-1 and VCAM-1 were higher in the aortic arch of HIV-1Tg rats compared to controls. Also, the level of sICAM-1 was elevated in the HIV-1Tg rats compared to controls, but the ICAM-1 gene expression profile did not show any differences between the groups. CONCLUSIONS/SIGNIFICANCE: HIV-1Tg rats have gene expression patterns indicating endothelial dysfunction and accelerated atherosclerosis in aorta, suggesting that HIV-infection per se may cause atherosclerosis. This transgenic rat model may be a very promising model for further studies of the pathophysiology behind HIV-associated cardiovascular disease.

Prevalence of extended-spectrum cephalosporinase (ESC)-producing Escherichia coli in Danish slaughter pigs and retail meat identified by selective enrichment and association with cephalosporin usage

DEFF Research Database (Denmark)

Agersø, Yvonne; Aarestrup, Frank Møller; Pedersen, Karl

2012-01-01

OBJECTIVES: To investigate the prevalence of extended-spectrum cephalosporinase (ESC)-producing Escherichia coli in pigs at slaughter and retail meat, and possible associations with the consumption of third- and fourth-generation cephalosporins. METHODS: During 2009, faecal samples from Danish pigs...... (n = 786) were collected at slaughter, and 866 meat samples [Danish: pork (153), broiler meat (121) and beef (142); and imported: pork (173), broiler meat (193) and beef (84)] were randomly collected in retail stores and outlets. E. coli was isolated after enrichment in MacConkey broth.......7%–3.3% in other meat types. ESC E. coli from imported broiler meat (n = 69) contained blaCMY-2 (48%), blaCTX-M-1 (25%) and blaSHV-12 (16%). Without selective enrichment, no ESC E. coli from pigs and only 4.1% from imported broiler meat were found. CONCLUSIONS: The usage of cephalosporins for slaughter pigs may...

STS-69 postflight presentation

Science.gov (United States)

1995-10-01

A postflight conference of the STS-69 mission is presented. The flightcrew ('The Dog Team') consisted of Cmdr. David Walker, Pilot Kenneth Cockrell, Payload Cmdr. James Voss, and Mission Specialists James Newman and Michael Gernhardt. The mission's primary objective was the deployment and retrieval of the SPARTAN-201 satellite, which investigated the interaction between the Sun and it's solar wind. Other secondary experiments and shuttle payloads included the Wake Shield Facility (WSF), which grew several layers of semiconductor films, the International Extreme Ultraviolet Hitchhiker (IEH-1), the Capillary Pumped Loop-2/Gas Bridge Assembly (CAPL-2/GBA), several Get Away Specials (GAS) experiments, the Electrolysis Performance Improvement Concept Study (EPICS), the Thermal Energy Storage (TES-2) experiment, the Commercial Generic Bioprocessing Apparatus-7 (CGBA-7), the National Institutes of Health-Cells 4 (NIH-C4) experiment, and the Biological Research in Canister-6 (BRIC-6) experiment. Earth views consisted of Saudi Arabia water wells, uncommon vortices over Oman, the Amazon River, the Bahamas, Somalia, a sunset over the Earth's horizon, and two hurricanes, Luis and Marilyn.

Measurements of the Total-Cross-Section Difference ΔσL(np) at 1.39, 1.69, 1.89, and 1.99 GeV

International Nuclear Information System (INIS)

Sharov, V.I.; Anischenko, N.G.; Averichev, S.A.; Bartenev, V.D.; Blinov, N.A.; Borzunov, Yu.T.; Chernykh, E.V.; Chumakov, V.F.; Dolgii, S.A.; Fimushkin, V.V.; Golovanov, L.B.; Kirillov, A.D.; Komogorov, E.V.; Kovalenko, A.D.; Krasnov, V.A.; Ladygin, V.P.; Liburg, M.Yu.; Livanov, A.N.; Maniakov, P.K.; Matyushevsky, E.A.

2005-01-01

New accurate data of the neutron-proton spin-dependent total-cross-section difference Δσ L (np) at the neutron-beam kinetic energies 1.39, 1.69, 1.89, and 1.99 GeV are presented. In general, these data complete the measurements of energy dependence of Δσ L (np) over the Dubna Synchrophasotron energy region. Measurements were carried out at the Synchrophasotron of the Veksler and Baldin Laboratory of High Energies of the Joint Institute for Nuclear Research. The quasi-monochromatic neutron beam was produced by breakup of extracted polarized deuterons. The deuteron (and hence neutron) polarization direction was flipped every accelerator burst. The initial transverse (with respect to beam momentum) neutron polarization was changed to a longitudinal one and longitudinally polarized neutrons were transmitted through the large proton longitudinally polarized target. The target polarization direction was inverted after one to two days of measurements. Four different combinations of the beam and target parallel and antiparallel polarization directions, both oriented along the neutron-beam momentum, were used at each energy. A fast decrease in -Δσ L (np) with increasing energy above 1.1 GeV and a structure in the energy dependence around 1.8 GeV, first observed from our previous data, seem to be well revealed. The new results are also compared with model predictions and with phase-shift analysis fits. The Δσ L quantities for isosinglet state I = 0, deduced from the measured Δσ L (np) values and known Δσ L (pp) data, are also given. The results of the measurements of unpolarized total cross sections σ 0tot (np) at 1.3, 1.4, and 1.5 GeV and σ 0tot (nC) at 1.4 and 1.5 GeV are presented as well. These data were obtained using the same apparatus and high-intensity unpolarized deuteron beams extracted either from the Synchrophasotron or from the Nuclotron

Two wheat glutathione peroxidase genes whose products are located in chloroplasts improve salt and H2O2 tolerances in Arabidopsis.