scholarly journals Recognition of another member of the malignant catarrhal fever virus group: an endemic gammaherpesvirus in domestic goats

2001 ◽  
Vol 82 (1) ◽  
pp. 227-232 ◽  
Author(s):  
Hong Li ◽  
Janice Keller ◽  
Donald P. Knowles ◽  
Timothy B. Crawford
Keyword(s):  
Dna Polymerase ◽  
Sequence Alignment ◽  
Gene Sequence ◽  
Homologous Sequence ◽  
Malignant Catarrhal Fever ◽  
Polymerase Gene ◽  
Virus Sequence ◽  
Herpesvirus 1 ◽  
Alignment Analysis ◽  
Recognition Of Another

A novel gammaherpesvirus in goats that is herein tentatively designated as caprine herpesvirus-2 was identified based on the sequence of a fragment from the herpesvirus DNA polymerase gene. Sequence alignment analysis revealed that the virus sequence isolated from goats was 67% identical to the homologous sequence from alcelaphine herpesvirus-1, 71% identical to ovine herpesvirus-2 and 73% identical to a recently recognized herpesvirus causing malignant catarrhal fever in white-tailed deer. Combined serological and PCR-survey data demonstrated that this virus is endemic in goats and its transmission pattern may be similar to that of ovine herpesvirus-2 in sheep.

scholarly journals PENGELOMPOKKAN SEPULUH VARIETAS TEMBAKAU (Nicotiana tabacum) BERDASARKAN KERAGAMAN RUNUTAN BASA PARSIAL GEN PMT(PUTRESCINE N-METHYLTRANSFERASE) Clustering of ten tobacco (Nicotiana tabacum) varieties based on the partial PMT (putrescine N-methyltranfera

2017 ◽  
Vol 23 (1) ◽  
pp. 36
Author(s):  
Sesanti Basuki ◽  
Sudarsono Sudarsono
Keyword(s):  
Nicotiana Tabacum ◽  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Gene Sequence ◽  
Gene Sequences ◽  
Multiple Sequence ◽  
Multiple Sequence Alignment Analysis ◽  
Nicotine Level ◽  
Alignment Analysis ◽  
The Relationship

<p align="center">Abstrak</p><p>Gen <em>PMT</em> adalah gen penyandi enzim putresina N-metiltransferase (PMT) yang berperan dalam lintasan biosintesis nikotin pada tanaman tembakau (<em>Nicotiana tabacum</em>). Sepuluh varietas tembakau yang memiliki perbedaan tingkat kadar nikotin diuji untuk mempelajari: (1) keragaman runutan basa parsial gen <em>PMT</em> dari masing-masing varietas, dan (2) kekerabatan antara sepuluh varietas tembakau yang diuji berdasarkan keragaman runutan basa parsial gen <em>PMT</em>. Keragaman runutan basa dianalisis dengan mensejajarkan data runutan basa dari sepuluh varietas tembakau yang diuji dengan runutan basa dari <em>Ntpmt_Sindoro1</em> (JQ438825) yang telah tersimpan dalam <em>database</em><em> </em><em>genbank NCBI</em>. Hasil pensejajaran digunakan untuk menghitung matriks jarak, yang selanjutnya digunakan untuk menganalisis hubungan kekerabatan diantara sepuluh varietas tembakau. Hasil analisis memperlihatkan adanya variasi ukuran dan jumlah runutan basaparsial gen <em>PMT</em> asal sepuluh varietas tembakau yang dianalisis. Hasil analisis juga memperlihatkan bahwa runutan basa parsial gen <em>PMT</em> tersebut berasal/diturunkan dari sumber (<em>ancestor</em>) yang sama dan  terkait dengan biosintesis nikotin pada tembakau. Runutan basaparsial gen <em>PMT</em> dari sepuluh varietas yang dianalisis memisahkan antara kelompok tembakau introduksi (kadar nikotin rendah-sedang) dengan kelompok tembakau lokal (kadar nikotin sedang-tinggi). Dua kelompok memisah berdasarkan level kadar nikotin, danperbedaan/perubahan susunan basa pada situs-situs tertentu dari runutan basaparsial gen <em>PMT</em>  yang dianalisis. Informasi tentang mutasi yang terjadi pada situs-situs runutan basa dari parsial gen <em>PMT</em><em> </em>dapat digunakan untuk mempelajari keterkaitan antara perubahan basa pada fragmen gen <em>PMT</em> dengan kandungan nikotin total tembakau yang terjadi selama proses evolusi.</p><p>Kata kunci: Analisis pengelompokkan, gen <em>PMT,</em>Nikotin, <em>Nicotiana tabacum</em></p><p align="center"><strong> </strong></p><p align="center">Abstract</p><p><strong> </strong><em>PMT</em> gene is the gene encoded putrescine N-methiltransferase which is related to nicotine biosinthesis in tobacco (<em>Nicotiana  tabacum</em>). Ten tobacco varieties with different nicotine level were used inthis study. The aims of this study were: (1) to analyze thepartial <em>PMT</em> gene sequence diversity among ten tobacco varieties, and (2) to evaluate the closed-relationship amongten tobacco varieties based on their partial<em>PMT</em> gene sequences diversity.Sequence diversity was analyzed by multiple sequence alignment between the partial<em>PMT</em> gene sequence of the ten tobacco varietiesand <em>Ntpmt_Sindoro1 </em>sequence deposited in the NCBI gene-bank database.The phylogenetic relationship amongthe sequences was inferred by genetic distancebetween pairs of sequences using the pairwise and multiple sequence alignment analysis. Analysis of the sequences showed that all varieties analyzed had varied in size and number of the <em>PMT</em> gene fragments yielded. The analysis also revealed that thepartial<em>PMT</em> gene sequencesarecoming from the same ancestor which related to nicotine biosynthesis in tobacco. Phylogenetic analysis separated the partial<em>PMT</em> gene sequences into two different branches significantly (bootstrap value = 100), and clustered together based on tobacco types with different nicotine level in whichcould be due to some baseschanged on the specific sites of the<em>PMT</em> gene sequences.  This information could be used to study the relationship between some bases changed on the specific sites of the<em>PMT</em> gene sequences and the nicotine content variation yielded by the ten tobacco varieties that is happened during evolution time.</p><p>Key words: Clustering analysis, <em>PMT</em> gene, nicotine, <em>Nicotiana tabacum</em></p>

scholarly journals Detecting and isolating false negatives of SARS-CoV-2 primers and probe sets among the Japanese Population: A laboratory testing methodology and study

2020 ◽  
Author(s):  
Wataru Tsutae ◽  
Wirawit Chaochaisit ◽  
Hideyuki Aoshima ◽  
Chiharu Ida ◽  
Shino Miyakawa ◽  
...  
Keyword(s):  
Disease Control ◽  
Sequence Alignment ◽  
Japanese Population ◽  
Rt Pcr ◽  
False Negatives ◽  
Control And Prevention ◽  
Virus Sequence ◽  
Alignment Analysis ◽  
Effective Result ◽  
Higher Sensitivity

[Objectives] In this study, a comparative study between primers from Japan's and US's disease control centers was conducted. As further investigation, virus sequence alignment with primers' oligonucleotide was analyzed. [Design or methods] 11,652 samples from Japanese population were tested for SARS-CoV-2 positive using recommended RT-PCR primer-probe sets from Japan National Institute of Infectious Disease (NIID) and US Centers for Disease Control and Prevention (CDC). [Results] Of the 102 positive samples, 17 samples (16.7% of total positives) showed inconsistent results when tested simultaneously for the following primers: JPN-N2, JPN-N1, CDC-N1, and CDC-N2. As a result, CDC recommended primer-probe sets showed relatively higher sensitivity and accuracy. Further virus sequence alignment analysis showed evidences for virus mutation happening at primer's binding sites. [Conclusions] The inconsistency in the RT-PCR results for JPN-N1, JPN-N2, CDC-N1, and CDC-N2 primer-probe sets could be attributed to differences in virus mutation at primers' binding site as observed in sequence analysis. The use of JPN-N2 combined with CDC-N2 primer produces the most effective result to reduce false negatives in Japan region. In addition, adding CDC-N1 will also help to detect false negatives.

scholarly journals Newly Recognized Herpesvirus Causing Malignant Catarrhal Fever in White-Tailed Deer (Odocoileus virginianus)

2000 ◽  
Vol 38 (4) ◽  
pp. 1313-1318 ◽  
Author(s):  
Hong Li ◽  
Neil Dyer ◽  
Janice Keller ◽  
Timothy B. Crawford
Keyword(s):  
Odocoileus Virginianus ◽  
Clinical Signs ◽  
Malignant Catarrhal Fever ◽  
Polymerase Gene ◽  
Peripheral Blood Leukocytes ◽  
Degenerate Primers ◽  
Blood Leukocytes ◽  
Dna Fragment ◽  
Herpesvirus 1 ◽  
Viral Sequences

Malignant catarrhal fever (MCF) was diagnosed by clinical signs and lesions in five out of six white-tailed deer (Odocoileus virginianus) in a North American zoo. The clinical signs and histopathological lesions in these deer were typical of MCF. Antibody to an epitope conserved among the MCF viruses was detected in the sera collected from the deer. PCR failed to amplify viral sequences from DNA extracted from peripheral blood leukocytes (PBL) and/or spleens of the deer with primers specific for ovine herpesvirus 2 (OHV-2) or specific for alcelaphine herpesvirus 1 (AHV-1). By using degenerate primers targeting a conserved region of a herpesviral DNA polymerase gene, a DNA fragment was amplified from the PBL or spleens of all six deer and sequenced. Alignment of the sequences demonstrated that the virus in the deer belongs to the Gammaherpesvirinae subfamily, exhibiting 82% identity to OHV-2, 71% to AHV-1, and 60% to a newly identified bovine lymphotropic herpesvirus. This virus, which causes classical MCF in white-tailed deer, is a newly recognized agent belonging to the MCF group of gammaherpesviruses. It is the third reported pathogenic MCF virus, genetically distinct but closely related to OHV-2 and AHV-1. The reservoir for the virus has not been identified.

scholarly journals Genetic evidence for two protein domains and a potential new activity in bacteriophage T4 DNA polymerase.

Genetics ◽  
1990 ◽  
Vol 124 (2) ◽  
pp. 213-220 ◽  
Author(s):  
L J Reha-Krantz
Keyword(s):  
Dna Polymerase ◽  
Bacteriophage T4 ◽  
Rnase H ◽  
Ribonuclease H ◽  
Temperature Sensitive ◽  
Polymerase Gene ◽  
Dna Polymerase I ◽  
E Coli ◽  
Intragenic Complementation ◽  
Polymerase I

Abstract Intragenic complementation was detected within the bacteriophage T4 DNA polymerase gene. Complementation was observed between specific amino (N)-terminal, temperature-sensitive (ts) mutator mutants and more carboxy (C)-terminal mutants lacking DNA polymerase polymerizing functions. Protein sequences surrounding N-terminal mutation sites are similar to sequences found in Escherichia coli ribonuclease H (RNase H) and in the 5'----3' exonuclease domain of E. coli DNA polymerase I. These observations suggest that T4 DNA polymerase, like E. coli DNA polymerase I, contains a discrete N-terminal domain.

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