1,721,111 research outputs found
Complete genome sequence of a putative new caulimovirus which exists as endogenous pararetroviral sequences in Angelica dahurica
No full textA virus isolate designated Angelica bushy stunt virus (AnBSV), provisionally representing a new species in the genus Caulimovirus, was discovered in the medicinal plant Angelica dahurica. The complete 8,300-nt genomic DNA of AnBSV had seven putative open reading frames containing conserved domains/motifs, which are typical features of caulimoviruses, and showed the greatest nucleotide sequence identity (74% identity and 27% query coverage) to a lamium leaf distortion virus isolate. Interestingly, the new caulimovirus exists as endogenous pararetroviral sequences in the host plant and is considered to have multiple defective plant genome-integrated copies that may lead to the generation of subgenomic DNA species
First report of soybean yellow mottle mosaic virus in soybean in North America
No full textSoybean yellow mottle mosaic virus (SYMMV) is a soybean-infecting virus recently discovered in Korea that initially induces bright yellow mosaic on leaves followed by stunting and reduced growth of older leaves (1). Nucleotide sequence analysis of genomic RNA of the Korean SYMMV isolate suggested that the virus is a new member of the genus Carmovirus in the family Tombusviridae. To determine whether SYMMV is present in the United States, single leaflets were collected without regard for symptoms from 7 to 10 plants in each of 136 plots in August 2008 from a research field in Stoneville, MS that contained 16 plant introductions (including five from Korea) and 'Williams 82'. Samples were grouped into 10 pools of 100 leaves from which total RNA was extracted with the Qiagen RNeasy Plant Mini Kit (Germantown, MD), reverse transcribed, and amplified with SuperScript III Platinum SYBR Green One-Step Quantitative Real-time Reverse Transcriptase-PCR Kit (Invitrogen, Carlsbad, CA) and two pairs of oligonucleotide primers (5'-CGTCTGCCAGGGTTTAATACTA-3', and 5'-GATTAGCATGTCAGGGTGGTCG-3'; and 5'-ACTGAGTCCCCTGCTTAT-3' and 5'-CATCACTAGCGTCYGGATCA-3') that were designed from regions conserved between SYMMV and Cowpea mottle virus (CPMoV; a related and seed-transmitted carmovirus). Six 100-leaflet pools were positive with both primer sets and four pools were negative with both primer sets. Total RNA extracted from one positive pool was reverse transcribed using SuperScript II reverse transcriptase and a primer complementary to nt 4,000 to 4,009 of the SYMMV genome and amplified using iProof DNA polymerase (Bio-Rad, Hercules, CA) as two overlapping DNA fragments using primers corresponding to nt 1 to 21 and complementary to nt 3,483 to 3,508 and corresponding to nt 3,366 to 3,391 and complementary to nt 4,000 to 4,009. DNA fragments were sequenced using a BigDye Terminator Cycle Sequencing Kit and ABI 3730XL capillary sequencers (Applied Biosystems, Foster City, CA). The 4,009-nt sequence of the Mississippi SYMMV isolate (GenBank Accession No. FJ707484) was 96% identical to the Korean SYMMV isolate and 65% identical to CPMoV. Because of the sampling techniques used, it was not possible to associate SYMMV-positive plants with disease symptoms in Mississippi. To our knowledge, this is the first report of SYMMV in North America. Reference: (1) M. Nam et al. Online publication. doi:10.1077/s00705-009-0480. Arch. Virol., 2009.open
Synthesis and antifungal activity of a novel series of 13-(4-isopropylbenzyl)berberine derivatives
No full textBy replacing the methyl group of 13-(4-isopropylbenzyl)berberine 2 with various acyl, alkyl, and benzyl groups via the demethylated intermediate, 13-(4-isopropylbenzyl)berberrubine 4, a novel series of 9-O-alkyl-13-(4- isopropylbenzyl)berberine derivatives was synthesized and examined for antifungal activities against various human pathogenic fungi. The introduction of various alkyl groups led to enhanced antifungal activity but that of acyl groups resulted in decrease of the activity. Among them, 9-O-butyl-13-(4- isopropylbenzyl)berberine 6d exhibited the most potent antifungal activities against Cryptococcus neoformans, Candida species (MIC = 0.25-1 μg/ml), and Aspergillus species (MIC = 2-4 μg/ml). The compound was found to be relatively safe up to 900 mg/kg in oral administration to mice.open
Monitoring of horizontal gene transfer from agricultural microorganisms to soil bacteria and analysis of microbial community in soils
No full textTo investigate the possibility of horizontal gene transfer between agricultural microorganisms and soil microorganisms in the environment, Bacillus subtilis KB producing iturin and the PGPR recombinant strain Pseudomonas fluorescens MX1 were used as model microorganisms. The soil samples of cucumber or tomato plants cultivated in pots and the greenhouse for a six month period were investigated by PCR, real-time PCR, Southern hybridization, and terminal restriction fragment length polymorphism (T-RFLP) fingerprinting. Our data from Southern blotting and TRFLP patterns suggest that the model bacteria do not give significant impacts on the other bacteria in the pots and greenhouse during cultivation.open
Complete genome sequence of a South Korean isolate of Habenaria mosaic virus
No full textHabenaria mosaic virus (HaMV), a member of the genus Potyvirus in the family Potyviridae, was first discovered from Habenaria
radiata in Japan. The complete genomic sequence of a South Korean isolate (PA1) of HaMV infecting Plantago asiatica L.
was determined with high-throughput RNA sequencing.open
Genome sequence of a recombinant brassica yellows virus infecting Chinese cabbage
No full textRNA from a Chinese cabbage plant (Brassica campestris ssp. pekinensis) showing leaf malformation and mottling was labeled and hybridized to a DNA chip capable of detecting plant viruses and viroids. Probes specific for beet mild yellowing virus (BMYV) and beet western yellows virus (BWYV) yielded positive results, suggesting that the plant was infected by a polerovirus. Primers designed from the sequences of the positive probes were used to amplify and sequence one portion of the viral genome. This sequence showed a 90 % or greater identity to several poleroviruses, including BMYV, BWYV, beet chlorosis virus (BChV) and turnip yellows virus (TuYV). The complete genome sequence of the Chinese cabbage-infecting polerovirus consisted of 5,666 nt and was most closely related to brassica yellows virus (BrYV; 94 % identity). The virus was named BrYV-Cheongsong (BrYV-CS). However, ORF3, ORF4 and the 5′ half of ORF5 of BrYV-CS were more closely related to those of TuYV, BWYV, BChV and BMYV than to those of BrYV. Interestingly, a recombination event (positions 3531-4819 in BrYV-CS) was detected when this sequence was aligned with those of BrYV and TuYV. This region showed the highest sequence identity to that of TuYV (94 % identity) and had greater than 93 % identity to those of BWYV, BChV and BMYV, but it shared only 81 % identity with that of BrYV. Taken together, the genomes of BrYV-CS and BrYV are closely related. However, the structural genes in the 3′ half of the genome of BrYV-CS are more closely related to those of other poleroviruses.open
Nucleotide sequence and genome organization of a new proposed crinivirus, tetterwort vein chlorosis virus
No full textThe genome of tetterwort vein chlorosis virus (TVCV) from South Korea has been completely sequenced. Its genomic organization resembles those of other criniviruses, with several new features, indicating that TVCV is a member of a new species in the genus Crinivirus, family Closteroviridae. RNA1 contains 8467 nucleotides, with at least four opening reading frames (ORFs). ORF1a encodes a protein with predicted papain-like protease, methyltransferase, and helicase activities. ORF1b encodes a putative RNA-dependent RNA polymerase that is apparently expressed through a +1 ribosomal frameshift. RNA2 contains 8113 nucleotides encoding at least nine proteins, similar to most crinivirus RNA2s. The 3′ untranslated regions of the bipartite RNA genome share 82.1 % nucleotide sequence identity.open
Nucleotide sequence and genome organization of atractylodes mottle virus, a new member of the genus Carlavirus
No full textThe complete genome sequence of a member of a distinct species of the genus Carlavirus in the family Betaflexiviridae, tentatively named atractylodes mottle virus (AtrMoV), has been determined. Analysis of its genomic organization indicates that it has a single-stranded, positive-sense genomic RNA of 8866 nucleotides, excluding the poly(A) tail, and consists of six open reading frames typical of members of the genus Carlavirus. The individual open reading frames of AtrMoV show moderately low sequence similarity to those of other carlaviruses at the nucleotide and amino acid sequence levels. Pairwise comparison and phylogenetic analysis suggest that AtrMoV is most closely related to chrysanthemum virus B.open
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