Cloning and sequence analysis of the plasmid DNA found in Rhizoctonia solani AG-2-2 LP isolate and its potential use for fungal detection

Mycoscience ◽  
1999 ◽  
Vol 40 (1) ◽  
pp. 29-33
Author(s):  
Susumu Takamatsu ◽  
Manami Nakano ◽  
Kaewalin Kunasakdakul ◽  
Hideyuki Yokota ◽  
Hitoshi Kunoh
Keyword(s):  
Sequence Analysis ◽  
Rhizoctonia Solani ◽  
Plasmid Dna ◽  
Potential Use

Detection of Rhizoctonia solani AG-2-2 IV, the Causal Agent of Large Patch of Zoysiagrass, Using Plasmid DNA as a Probe.

1998 ◽  
Vol 64 (5) ◽  
pp. 451-457 ◽  
Author(s):  
Susumu TAKAMATSU ◽  
Manami NAKANO ◽  
Hideyuki YOKOTA ◽  
Hitoshi KUNOH
Keyword(s):  
Rhizoctonia Solani ◽  
Plasmid Dna ◽  
Causal Agent ◽  
Large Patch

scholarly journals In Vitro Gene Delivery Mediated by Asialofetuin-Appended Cationic Liposomes Associated with γ-Cyclodextrin into Hepatocytes

2011 ◽  
Vol 2011 ◽  
pp. 1-13 ◽  
Author(s):  
Keiichi Motoyama ◽  
Yoshihiro Nakashima ◽  
Yukihiko Aramaki ◽  
Fumitoshi Hirayama ◽  
Kaneto Uekama ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Gene Delivery ◽  
Plasmid Dna ◽  
Transfection Efficiency ◽  
Cationic Liposomes ◽  
Nonviral Vector ◽  
Liposomal Membrane ◽  
Transfer Activity ◽  
Potential Use

The purpose of this study is to evaluate in vitro gene delivery mediated by asialofetuin-appended cationic liposomes (AF-liposomes) associating cyclodextrins (CyD/AF-liposomes) as a hepatocyte-selective nonviral vector. Of various CyDs, AF-liposomes associated with plasmid DNA (pDNA) and γ-cyclodextrin (γ-CyD) (pDNA/γ-CyD/AF-liposomes) showed the highest gene transfer activity in HepG2 cells without any significant cytotoxicity. In addition, γ-CyD enhanced the encapsulation ratio of pDNA with AF-liposomes, and also increased gene transfer activity as the entrapment ratio of pDNA into AF-liposomes was increased. γ-CyD stabilized the liposomal membrane of AF-liposomes and inhibited the release of calcein from AF-liposomes. The stabilizing effect of γ-CyD may be, at least in part, involved in the enhancing gene transfer activity of pDNA/γ-CyD/AF-liposomes. Therefore, these results suggest the potential use of γ-CyD for an enhancer of transfection efficiency of AF-liposomes.

scholarly journals Functional and genetic characterization of an incF-type multidrug resistance plasmid isolated from fresh spinach

2018 ◽  
Author(s):  
Adeyinka O. Ajayi ◽  
Benjamin J. Perry ◽  
Christopher K. Yost
Keyword(s):  
Antibiotic Resistance ◽  
Multidrug Resistance ◽  
Food Safety ◽  
Sequence Analysis ◽  
Dna Sequence ◽  
Resistance Genes ◽  
Plasmid Dna ◽  
Antibiotic Resistance Genes ◽  
Multidrug Resistant ◽  
Leafy Greens

AbstractThe presence of antibiotic-resistant bacteria and clinically-relevant antibiotic resistance genes within raw foods is an on-going food safety concern. It is particularly important to be aware of the microbial quality of fresh produce because foods such as leafy greens including lettuce and spinach are minimally processed and often consumed raw therefore they often lack a microbial inactivation step. This study characterizes the genetic and functional aspects of a mobile, multidrug resistance plasmid, pLGP4, isolated from fresh spinach bought from a farmers’ market. pLGP4 was isolated using a bacterial conjugation approach. The functional characteristics of the plasmid were determined using multidrug resistance profiling and plasmid stability assays. pLGP4 was resistant to six of the eight antibiotics tested and included ciprofloxacin and meropenem. The plasmid was stably maintained within host strains in the absence of an antibiotic selection. The plasmid DNA was sequenced using an Illumina MiSeq high throughput sequencing approach and assembled into contigs using SPAdes. PCR mapping and Sanger DNA sequencing of PCR amplicons was used to complete the plasmid DNA sequence. Comparative sequence analysis determined that the plasmid was similar to plasmids that have been frequently associated with multidrug resistant clinical isolates of Klebsiella spp. DNA sequence analysis showed pLGP4 harboured qnrB1 and several other antibiotic resistance genes including three β-lactamases: blaTEM-1, blaCTX-M-15 and blaOXA-1. The detection of a multidrug-resistant, clinically-relevant plasmid on fresh spinach emphasizes the importance for vegetable producers to implement evidence-based food safety approaches into their production practises to ensure the food safety of leafy greens.

Genes involved in protein metabolism of the probiotic lactic acid bacterium Lactobacillus delbrueckii UFV H2b20

2011 ◽  
Vol 2 (3) ◽  
pp. 209-220 ◽  
Author(s):  
A. Do Carmo ◽  
D. da Silva ◽  
M. De Oliveira ◽  
A. Borges ◽  
A. De Carvalho ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Sequence Analysis ◽  
Lactobacillus Delbrueckii ◽  
Schematic Model ◽  
Protein Sequence Analysis ◽  
Branched Chain Amino Acid ◽  
History Of ◽  
Branched Chain ◽  
Oligopeptide Transport System ◽  
Potential Use

A basic requirement for the prediction of the potential use of lactic acid bacteria (LAB) in the dairy industry is the identification of specific genes involved in flavour-forming pathways. The probiotic Lactobacillus delbrueckii UFV H2b20 was submitted to a genetic characterisation and phylogenetic analysis of genes involved in protein catabolism. Eight genes belonging to this system were identified, which possess a closely phylogenetic relationship to NCFM strains representative, as it was demonstrated for oppC and oppBII, encoding oligopeptide transport system components. PepC, PepN, and PepX might be essential for growth of LAB, probiotic or not, since the correspondent genes are always present, including in L. delbrueckii UFV H2b20 genome. For pepX gene, a probable link between carbohydrate catabolism and PepX expression may exists, where it is regulated by PepR1/CcpA-like, a common feature between Lactobacillus strains and also in L. delbrueckii UFV H2b20. The well conserved evolutionary history of the ilvE gene is evidence that the pathways leading to branched-chain amino acid degradation, such as isoleucine and valine, are similar among L. delbrueckii subsp. bulgaricus strains and L. delbrueckii UFV H2b20. Thus, the involvement of succinate in flavour formation can be attributed to IlvE activity. The presence of aminopeptidase G in L. delbrueckii UFV H2b20 genome, which is absent in several strains, might improve the proteolytic activity and effectiveness. The nucleotide sequence encoding PepG revealed that it is a cysteine endopeptidase, belonging to Peptidase C1 superfamily; sequence analysis showed 99% identity with L. delbrueckii subsp. bulgaricus ATCC 11842 pepG, whereas protein sequence analysis revealed 100% similarity with PepG from the same organism. The present study proposes a schematic model to explain how the proteolytic system of the probiotic L. delbrueckii UFV H2b20 works, based on the components identified so far.

Mycelial Interactions and the Potential Use of Tuft Formation in Characterizing Rhizoctonia solani Isolates Infecting Cereals

1993 ◽  
Vol 41 (2) ◽  
pp. 253 ◽  
Author(s):  
HA Yang ◽  
K Sivasithamparam ◽  
PA Obrien
Keyword(s):  
Rhizoctonia Solani ◽  
Anastomosis Group ◽  
Potato Dextrose Agar ◽  
Bare Patch ◽  
Field Isolates ◽  
Mycelial Interactions ◽  
Causal Pathogen ◽  
Patch Disease ◽  
Potential Use ◽  
Compatible Interactions

Field isolates of Rhizoctonia solani anastomosis group (AG) 8, the most important causal pathogen of cereal bare-patch disease, were paired with each other and with tester strains of other AGs on potato-dextrose agar amended with charcoal (PDCA) to investigate mycelial interactions. Pairings among AG 8 field isolates produced compatible interactions of either tuft or merging reactions. Tufts formed between all paired field isolates from different pectic zymogram groups (ZGs) within AG 8, but pairings between genetically identical isolates showed merging reactions. Pairings of AG 8 field isolates with the tester strains of the other AGs led to incompatible interactions varying from merging line to barrage reactions. As formation of a tuft indicates that the paired isolates are able to anastomose and to form viable heterokaryons, the testing of mycelial interaction types, highlighted by tuft formation, may be used as a rapid procedure to characterise field isolates of R. solani obtained from cereals.

scholarly journals Diversity and Aggressiveness of Rhizoctonia solani and Rhizoctonia-like Fungi on Vegetables in New York

Plant Disease ◽  
2009 ◽  
Vol 93 (6) ◽  
pp. 615-624 ◽  
Author(s):  
Mana Ohkura ◽  
George S. Abawi ◽  
Christine D. Smart ◽  
Kathie T. Hodge
Keyword(s):  
New York ◽  
Sequence Analysis ◽  
Rhizoctonia Solani ◽  
Internal Transcribed Spacer ◽  
Anastomosis Group ◽  
Internal Transcribed Spacer Region ◽  
Snap Bean ◽  
First Report ◽  
Pathogenicity Tests ◽  
Waitea Circinata

Vegetable growers in New York, especially those growing table beets, have recently observed that the corn rotation is no longer effective in suppressing diseases caused by Rhizoctonia solani and Rhizoctonia-like fungi. To investigate this problem, 68 isolates of Rhizoctonia solani and Rhizoctonia-like fungi infecting vegetables in New York were isolated, characterized, and their pathogenicity on corn determined. Sequence analysis of the rDNA internal transcribed spacer region inferred 26 isolates to belong to R. solani anastomosis group (AG) 2-2 and 19 isolates to belong to AG 4. Remaining isolates belonged to AG 1, AG 2-1, AG 5, AG 11, Ceratobasidium AG (CAG) 2, CAG 6, and Waitea circinata var. zeae. This is a first report of AG 11 and W. circinata var. zeae recovered from naturally infected vegetables in New York. Pathogenicity tests on corn showed that the majority of isolates are pathogenic on corn, and isolates belonging to AG 2-2, AG 5, and AG 11 exhibited high aggressiveness. These results suggest that certain strains of R. solani and Rhizoctonia-like fungi infecting vegetables in New York have acquired the ability to infect corn. In addition, snap bean was inoculated with seven isolates exhibiting low to high aggressiveness on corn, and a correlation between aggressiveness on corn and snap bean was observed.

scholarly journals Antimicrobial Activity of Bacteria Isolated From the Rhizosphere and Phyllosphere of Avena Fatua and Brachiaria Reptans Growing in Heavy-Metal Polluted Environment

2021 ◽  
Author(s):  
Muskan Ali ◽  
Sadia Walait ◽  
Muhammad Farhan Ul Haque ◽  
Salma Mukhtar
Keyword(s):  
Heavy Metal ◽  
Antimicrobial Activity ◽  
Sequence Analysis ◽  
Plasmid Dna ◽  
Contaminated Soils ◽  
Avena Fatua ◽  
Whole Genome Sequence ◽  
Trna Genes ◽  
Bacterial Strains ◽  
16S Rrna Sequence

Abstract Environmental pollution especially heavy metal contaminated soils adversely affect the microbial communities associated with the rhizosphere and phyllosphere of plants growing in these areas. In the current study, we identified and characterized the rhizospheric and phyllospheric bacterial strains from Avena fatua and Brachiaria reptans with the potential for antimicrobial activity and heavy metal resistance. A total of 18 bacterial strains from the rhizosphere and phyllosphere of A. fatua and 19 bacterial strains from the rhizosphere and phyllosphere of B. reptans were identified based on 16S rRNA sequence analysis. Bacterial genera, including Bacillus, Staphylococcus, Pseudomonas and Enterobacter were dominant in the rhizosphere and phyllosphere of A. fatua and Bacillus, Marinobacter, Pseudomonas, Enterobacter, and Kocuria were the dominating bacterial genera from the rhizosphere and phyllosphere of B. reptans. Most of the bacterial strains were resistant to heavy metals (Cd, Pb and Cr) and showed antimicrobial activity against different pathogenic bacterial strains. The whole genome sequence analysis of Pseudomonas putida BR-PH17 was performed by using Illumina sequencing approach. The BR-PH17 genome contained a chromosome with size of 5774330 bp and a plasmid DNA with 80360 bp. In this genome, about 5368 predicted protein coding sequences with 5539 total genes, 22 rRNAs and 75 tRNA genes were identified. Functional analysis of chromosomal and plasmid DNA revealed a variety of enzymes and proteins involved in antibiotic resistance and biodegradation of complex organic pollutants. These results indicated that bacterial strains identified in this study could be utilized for bioremediation of heavy metal contaminated soils and as a novel source of antimicrobial drugs.

Plasmid Sequence Analysis from Long Reads v2

2021 ◽  
Author(s):  
David A Eccles
Keyword(s):  
Sequence Analysis ◽  
Plasmid Dna ◽  
De Novo ◽  
Consensus Sequence ◽  
Fasta File ◽  
High Quality ◽  
Plasmid Sequence ◽  
Long Reads ◽  
The Moment

This protocol demonstrates how to assemble reads from plasmid DNA, and generate a circularised and non-repetitive consensus sequence At the moment, this protocol uses Canu to de-novo assemble high-quality single-cut reads. Input(s): demultiplexed fastq files (see protocol Demultiplexing Nanopore reads with LAST). I've noticed that the default demultiplexing carried out by Guppy (at least up to v4.2.2, as used in the first version of this protocol) has issues with chimeric reads, which can affect assembly. Output(s): Consensus sequence per barcode as a fasta file

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