1,722,332 research outputs found
Integrated Jingmenvirus Polymerase Gene in Ixodes ricinus Genome
No full textMembers of the jingmenviruses group have been found in arthropods and mammals on all continents except Australia and Antarctica. Two viruses of this group were isolated from patients with fever after a tick bite. Using a nested RT-PCR assay targeting a jingmenvirus polymerase gene fragment, we screened ticks collected in seven regions of Russia and found that the abundant jingmenvirus-positive were of Ixodes ricinus species, with the prevalence ranging from 19.8% to 34.3%. In all cases, DNase/RNase treatment suggested that the detected molecule was DNA and subsequent next generation sequencing (NGS) proved that the viral polymerase gene was integrated in the I. ricinus genome. The copy number of the integrated polymerase gene was quantified by qPCR relative to the ITS2 gene and estimated as 1.32 copies per cell. At least three different genetic variants of the integrated polymerase gene were found in the territory of Russia. Phylogenetic analysis of the integrated jingmenvirus polymerase gene showed the highest similarity with the sequence of the correspondent gene obtained in Serbia from I. ricinus
Cloning of thermostable DNA polymerase gene from hyperthermophilic marine arcahea
No full textAn extremely thermophilic archaeal strains, NA2 was isolated from a deep-sea hydrothermal vent area at the PACMANUS field (3° 14' S, 151° 42' E) in the East Manus Basin. On the basis of 16S rRNA gene sequences, the NA2 belonged to genus Pyrococcus. The α-like DNA polymerase gene was screened from genomic library of Pyrococcus sp. NA002 by colony and southern blot analysis using the partial DNA polymerase gene segment. We have obtained six positive clones from 196 clones and one clone (#2-D4) has been chosen for further analysis. The inserted DNA (30 kb) of the #2-D4 clone was fully sequenced and we found the coding region of the α-like DNA polymerase gene. The open reading frame was 2,328 nucleotides and predicted amino acid sequence from the ORF had two conserved regions. One was the 3'-5' exonuclease motif consisting of ExoⅠ, Ⅱ, and Ⅲ, which is responsible for proofreading ability (repair system). The other region was the DNA polymerase domain consisting of six regions (region Ⅰ to Ⅵ) that are conserved among α-like DNA polymerases. The DNA polymerase gene is under cloning and expression by using a pET vector system.2
Cloning and characterization of a thermostable DNA polymerase gene
No full textAn extremely thermophilic archaeal strains, NA2 was isolated from a deep-sea hydrothermal vent area at the PACMANUS field (3° 14' S, 151° 42' E) in the East Manus Basin. On the basis of 16S rRNA gene sequences, the NA2 belonged to genus Pyrococcus. The α-like DNA polymerase gene was screened from a genomic library of Pyrococcus sp. NA2 by colony and southern hybridization using the partial DNA polymerase gene segment as a probe. We have obtained six positive clones from 196 clones and one clone (#2-D4) has been chosen for further analysis. The nucleotide sequence of the insert DNA (30kb) of the clone was determined and the coding region of the α-like DNA polymerase gene was found by using ORF finder. The DNA polymerase gene was 2,325 nucleotides in length and the translated protein had two conserved regions. One was the 3'-5' exonuclease motif consisting of ExoⅠ, Ⅱ, and Ⅲ. The other region was the DNA polymerase domain consisting of six regions (region Ⅰ to Ⅵ) conserved among α-like DNA polymerases. In a pairwise alignment, the amino acid sequence from NA2 showed highest identities to the following family B DNA polymerases of Pyrococcus sp. ST700 Pol B (GeneBank accession no. AJ250332) (94% identity), of P. abyssi ST855 Pol B (GeneBank accession no. Z54174) (89% identity), of T. kodakaransis KOD1 Pol B (GeneBank accession no. D29671) (78% identity), and of Crenarchaeota Pyrodictium occulum Pol B (GeneBank accession no. E10436) (33% identity).1
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Identification, Localization, Transcription, and Sequence Analysis of the Choristoneura fumiferana Nuclear Polyhedrosis Virus DNA Polymerase Gene
No full textAbstractThe location of the Choristoneura fumiferana baculovirus DNA polymerase gene was determined by hybridization analysis using a probe prepared from the previously identified polymerase gene from the Autographa californica multiple nuclear polyhedrosis virus. DNA sequence analysis revealed that the Choristoneura fumiferana baculovirus DNA polymerase gene consists of 2970 base pairs encoding 990 amino acids (114.2 kDa). Transcriptional analysis demonstrated that overlapping transcripts of 3.2 and 4.6 kb, first detected at 6 hr postinfection, potentially coded for the DNA polymerase gene. The major transcription starts sites, identified at 6 hr postinfection, mapped to baculovirus consensus early start sites CGTGCTCA and CAGT. The relatively low level and late initiation of the DNA polymerase gene coupled with our previous data on the temporal control of DNA replication and late gene synthesis (Liu and Carstens, 1993) suggests that the tow virulence of the spruce budworm baculovirus may be related to the regulation of its gene expression at the transcriptional level
Turkey coronavirus polymerase gene and genome transcription
No full textTurkey coronavirus (TCoV) is a group 3 coronavirus in the family Coronaviridae. However, little is known about TCoV genome and genome transcription. The objectives of this study were to investigate polymerase gene and genome transcription of TCoV. Sequences of polymerase gene and full-length genome of TCoV were completed for isolates 540 and ATCC. The genome contains 27749 nucleotides (nt) for 540 and 27816-nt for ATCC, excluding poly (A) tail. Thirteen open reading frames (ORF) were predicted for TCoV genome. Polymerase gene consists of ORF1a and ORF1b. Polyprotein 1a was predicted to be produced from ORF1a and polyprotein 1ab was produced from ORF1a and ORF1b via frameshift translation. Ten and fourteen nonstructure proteins were predicted and assigned to polyprotein 1a and 1ab, respectively. Phylogenetic analysis revealed 86.3% genome sequence identity between TCoV and avian infectious bronchitis virus (IBV), another group 3 coronavirus, further supporting a close relationship between the two. Six subgenomic mRNAs (sgRNA) were transcribed by TCoV with sg3UTR as an unpredicted sgRNA for 3’ untranslated region (UTR). The discovery of sg3UTR reduced predicted 3’UTR from about 500-nt to 300-nt. Five sgRNA were detected for spike gene and all of them differentiate only at transcription-regulating sequence. The abundance of (−) sgRNA was more than that of (+) sgRNA in TCoV infected tissues. Non-structure protein 15 (nsp15) of TCoV polyprotein was a novel endoribonuclease (NendoU) preferring cleaving U-containing ssRNA. Unlike other NendoU, TCoV nsp15 did not cleave dsRNA and did not require manganese or other divalent metal ions as cofactor. The active form of TCoV nsp15 was a homohexamer in vitro. In conclusion, TCoV has its genome organization similar to that of IBV and produces six sgRNA
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Phylogenetic tree of Otarine gammaherpesvirus DNA polymerase gene.
No full textPhylogenetic relationships of the DNA polymerase gene of Otarine gammaherpesvirus 1 (OtGHV1) and Otarine gammaherpesvirus 8 (OtGHV8) detected in South American fur seals (Arctocephalus australis) and South American sea lions (Otaria byronia), respectively, in Punta San Juan, Peru.</p
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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