scholarly journals The NLP Toxin Family in Phytophthora sojae Includes Rapidly Evolving Groups That Lack Necrosis-Inducing Activity

2012 ◽  
Vol 25 (7) ◽  
pp. 896-909 ◽  
Author(s):  
Suomeng Dong ◽  
Guanghui Kong ◽  
Dinah Qutob ◽  
Xiaoli Yu ◽  
Junli Tang ◽  
...  
Keyword(s):  
Positive Selection ◽  
Nicotiana Benthamiana ◽  
Plant Pathogens ◽  
Phytophthora Sojae ◽  
The Other ◽  
Death Process ◽  
Birth And Death Process ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Cyst Germination

Necrosis- and ethylene-inducing-like proteins (NLP) are widely distributed in eukaryotic and prokaryotic plant pathogens and are considered to be important virulence factors. We identified, in total, 70 potential Phytophthora sojae NLP genes but 37 were designated as pseudogenes. Sequence alignment of the remaining 33 NLP delineated six groups. Three of these groups include proteins with an intact heptapeptide (Gly-His-Arg-His-Asp-Trp-Glu) motif, which is important for necrosis-inducing activity, whereas the motif is not conserved in the other groups. In total, 19 representative NLP genes were assessed for necrosis-inducing activity by heterologous expression in Nicotiana benthamiana. Surprisingly, only eight genes triggered cell death. The expression of the NLP genes in P. sojae was examined, distinguishing 20 expressed and 13 nonexpressed NLP genes. Real-time reverse-transcriptase polymerase chain reaction results indicate that most NLP are highly expressed during cyst germination and infection stages. Amino acid substitution ratios (Ka/Ks) of 33 NLP sequences from four different P. sojae strains resulted in identification of positive selection sites in a distinct NLP group. Overall, our study indicates that expansion and pseudogenization of the P. sojae NLP family results from an ongoing birth-and-death process, and that varying patterns of expression, necrosis-inducing activity, and positive selection suggest that NLP have diversified in function.

scholarly journals Development of a Genoserotyping Method for Salmonella Infantis Detection on the Basis of Pangenome Analysis

2020 ◽  
Vol 9 (1) ◽  
pp. 67
Author(s):  
Seung-Min Yang ◽  
Jiwon Baek ◽  
Eiseul Kim ◽  
Hyeon-Be Kim ◽  
Seyoung Ko ◽  
...  
Keyword(s):  
Public Health ◽  
Polymerase Chain Reaction ◽  
Bacterial Species ◽  
Cost Effective ◽  
The Other ◽  
Gene Marker ◽  
Diagnostic Assay ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Substantial Economic Burden

In recent years, Salmonella Infantis has become a predominant serovariant in clinical and poultry isolates, thereby imposing a substantial economic burden on both public health and the livestock industry. With the aim of coping with the steep increase in serovar Infantis prevalence, a polymerase chain reaction (PCR)-based rapid and accurate diagnostic assay was developed in this study through pangenome profiling of 60 Salmonella serovars. A gene marker, SIN_02055, was identified, which is present in the S. Infantis genome but not in the pangenome of the other serovars. Primers specific to SIN_02055 were used to accurately detect serovar Infantis, and to successfully differentiate Infantis from the other 59 serovars in real-time PCR with a R2 of 0.999 and an efficiency of 95.76%. The developed method was applied to 54 Salmonella strains belonging to eight dominant serovars, and distinguished Infantis from the other seven serovars with an accuracy of 100%. The diagnostic primer set also did not show false positive amplification with 32 strains from eight non-Salmonella bacterial species. This cost-effective and rapid method can be considered an alternative to the classic serotyping using antisera.

scholarly journals Identification of Neisseria gonorrhoeae isolates with a recombinant porA gene in Scotland, United Kingdom, 2010 to 2011

2012 ◽  
Vol 17 (9) ◽  
Author(s):  
K Eastick ◽  
A Winter ◽  
S Jamdar
Keyword(s):  
Polymerase Chain Reaction ◽  
United Kingdom ◽  
Neisseria Gonorrhoeae ◽  
Sequence Type ◽  
The Other ◽  
Chain Reaction ◽  
Polymerase Chain

Three isolates of Neisseria gonorrhoeae have been identified in Scotland in 2010 and 2011, which lack sequences in the porA pseudogene commonly used as the target for confirmatory gonorrhoea polymerase chain reaction assays. Two isolates were clustered temporally and geographically and have the same sequence type and porA sequence. A similar strain was reported in Australia during early 2011. The other Scottish isolate was identified separately and is different in sequence type and porA sequence.

CHAPTER 60: Polymerase Chain Reaction for Detection of Systemic Plant Pathogens

2011 ◽  
pp. 341-359 ◽  
Author(s):  
A. Hadidi ◽  
A. Olmos ◽  
G. Pasquini ◽  
M. Barba ◽  
R. R. Martin ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Plant Pathogens ◽  
Chain Reaction ◽  
Polymerase Chain

Identification and diagnosis of Leishmania mexicana complex isolates by polymerase chain reaction

Parasitology ◽  
1994 ◽  
Vol 109 (4) ◽  
pp. 423-433 ◽  
Author(s):  
S. Eresh ◽  
S. M. McCallum ◽  
D. C. Barker
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Sequences ◽  
The Other ◽  
South American ◽  
Kinetoplast Dna ◽  
Leishmania Mexicana ◽  
Chain Reaction ◽  
Potential Host ◽  
Oligonucleotide Primers ◽  
Polymerase Chain

SUMMARYFollowing cloning of Leishmania (L.) amazonensis kinetoplast DNA two recombinant clones were identified: one specific for L. (L.) amazonensis and the other specific for L. (L.) amazonensis and closely related isolates. DNA sequences from these clones were compared with those of other kinetoplastids and oligonucleotide primers were designed to be used in the polymerase chain reaction. A pair of these primers has been shown not only to be highly specific for L. mexicana complex isolates but can also be used to distinguish between L. (L.) mexicana and L. (L.) amazonensis isolates. These primers have been tested with water-lysed cultures, crude DNA extracts from human patients, potential host reservoirs, sandfly vectors and with cell pellets after isoenzyme characterization. The results of these tests indicate that the primers can be used specifically in the presence of excess host DNA originating from the majority of South American countries.

scholarly journals Molecular Characterisation of Soil-Dwelling Bacillus thuringiensis using Transcriptional Regulator, XRE Gene and the Crystal Protein, cry2 gene

2021 ◽  
Vol 6 (1) ◽  
pp. 153-159
Author(s):  
E.O Akinyelure ◽  
◽  
D.A. Machido ◽  
H. I. Atta
Keyword(s):  
Bacillus Thuringiensis ◽  
Environmental Samples ◽  
Plant Pathogens ◽  
Transcriptional Regulator ◽  
Soil Samples ◽  
Molecular Techniques ◽  
Crystal Protein ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Sporulation Phase

Bacillus thuringiensis (Bt) is the organism that is used most frequently in biological pest management, which is distinguished by the capacity to possess crystalline inclusions throughout the sporulation phase. There is an increasing need to use biological control in controlling plant pathogens due to the inherent advantages. However, the detection of Bt has become more time consuming and cumbersome due to the numerous available crystal genes. The goal of the study was to isolate strains of Bacillus thuringiensis from the soil, characterise the isolates using the transcriptional regulator, XRE gene and the crystal proteins cry2gene and compare the efficiency of these two biomarkers in identifying Bt species. Five different Bacillus thuringiensis strains were isolated from soil samples in Zaria, Nigeria. Polymerase chain reaction was used to detect the existence of the cry2 and XRE genes. Four (80%) of the five isolates harboured the XRE genes, while none (0%) harboured the cry2 genes. This observation is a likely indication that the XRE gene is a reliable biomarker in the identification of Bt isolates from environmental samples. In order to ensure speed and reproducibility in the detection of Bt from environmental samples, molecular techniques targeting the XREgene are recommended. Keywords: Bacillus thuringiensis; transcriptional regulator, XRE; crystal protein, cry2

scholarly journals NATURE OF VARIABILITY OF CANDAHARIA LEVANDERI (SIMROTH, 1902) IN THE FERGHANA AND SURKHAN - SHERABAD VALLEYS, UZBEKISTAN

2021 ◽  
Vol 16 (4) ◽  
pp. 547-555
Author(s):  
Surayyo Sh. Abdurasulova ◽  
◽  
Аbduvaeit P. Pazilov ◽  
Keyword(s):  
Polymerase Chain Reaction ◽  
Climatic Conditions ◽  
The Other ◽  
Chain Reaction ◽  
Body Coloration ◽  
Polymerase Chain ◽  
The One ◽  
Two Populations

The variability of Candaharia levanderi (Simroth, 1902)(Gastropoda, Stylommatophora, Parmacellidae) in two biotopes (southern and northern slopes, the Kampirtepa gorges, the Kugitang Tau ridge) has been investigated using polymerase chain reaction (PCR) with the implementation of primers, the 18S DNA of the region is amplified, the variability (sharply differing in color) of two populations of C. levanderi is studied. The first population is in the suburbs of Namangan, (Namangan Region); the second population is in Kampirtepa gorges, Kugitang Tau ridge (Surkhandarya Region). It is established that, most often, the variability of morphological signs is observed on the coloration of mollusks. The development of body coloration is an adaptive feature that reflects the adaptability to certain biotopes on the one hand, and landscape and climatic conditions on the other.

Polymerase chain reaction and Q beta replicase amplification

1991 ◽  
Vol 37 (9) ◽  
pp. 1482-1485 ◽  
Author(s):  
P Cahill ◽  
K Foster ◽  
D E Mahan
Keyword(s):  
Polymerase Chain Reaction ◽  
Nucleic Acid ◽  
Mechanisms Of Action ◽  
The Other ◽  
Template Molecule ◽  
Chain Reaction ◽  
Signal Component ◽  
Pcr Method ◽  
Polymerase Chain ◽  
Target Sequences

Abstract The polymerase chain reaction (PCR) and Q beta replicase are two methods in which nucleic acid polymerases are used for amplification. Although these approaches share many similar problems concerning target contamination and probe specificity, they differ dramatically in their mechanisms of action and modes of application. The PCR method amplifies target sequences between two priming oligonucleotides and in essence amplifies a portion of the analyte. Q beta replicase, on the other hand, amplifies a specific template molecule hybridized to target sequences and therefore amplifies a signal component of the system. For this reason, Q beta replicase amplification has applications in areas other than for the detection of nucleic acid sequences. The requirements for application and the advantages of both PCR and Q beta replicase amplification are reviewed.

scholarly journals InvasiveStreptococcus pneumoniaeInfection Causing Hemolytic Uremic Syndrome in Children: Two Recent Cases

2003 ◽  
Vol 14 (6) ◽  
pp. 339-343 ◽  
Author(s):  
Otto G Vanderkooi ◽  
James D Kellner ◽  
Andrew W Wade ◽  
Tajdin Jadavji ◽  
Julian P Midgley ◽  
...  
Keyword(s):  
Hemolytic Uremic Syndrome ◽  
Shiga Toxin ◽  
The Other ◽  
Pfge Analysis ◽  
Chain Reaction ◽  
Toxin Assay ◽  
Uremic Syndrome ◽  
Polymerase Chain ◽  
Case Presentations ◽  
Shiga Toxin Genes

INTRODUCTION:Streptococcus pneumoniaeis an uncommon cause of hemolytic uremic syndrome (HUS) with a unique pathophysiology that differs from Shiga toxin-related HUS.METHODS: Case descriptions for each patient are provided. Each strain ofS pneumoniaewas subjected to a pulsed-field gel electrophoresis (PFGE) analysis, Shiga toxin assay and polymerase chain reaction to detect Shiga toxin genes. A review of the current literature was conducted.CASE PRESENTATIONS: Two patients withS pneumoniae-related HUS that presented to the Alberta Children's Hospital, Calgary, Alberta, within four weeks of each other in 2001 are described. Both presented with pneumonia and empyema with associated HUS. Both patients required dialysis, one patient for 10 days and the other for 18 days. Neither patient demonstrated evidence of Shiga toxin-related disease.S pneumoniaeisolated from blood or pleural fluid was penicillin susceptible. One isolate was serotype 3 and the other was serotype 14. The two strains had different PFGE patterns. Both patients recovered well with no persistent renal dysfunction.CONCLUSIONS:S pneumoniaecontinues to be an uncommon but important cause of HUS. Most cases can be confirmed or at least considered probable without performing a renal biopsy.

Expression of the integrin alpha 6 beta 4 in peripheral nerves: localization in Schwann and perineural cells and different variants of the beta 4 subunit

1994 ◽  
Vol 107 (2) ◽  
pp. 543-552 ◽  
Author(s):  
C.M. Niessen ◽  
O. Cremona ◽  
H. Daams ◽  
S. Ferraresi ◽  
A. Sonnenberg ◽  
...  
Keyword(s):  
Central Nervous System ◽  
Polymerase Chain Reaction ◽  
Nervous System ◽  
Peripheral Nerves ◽  
Northern Blot Analysis ◽  
The Other ◽  
Chain Reaction ◽  
The Central Nervous System ◽  
Polymerase Chain ◽  
Integrin Alpha 6

Integrin alpha 6 beta 4 is expressed in human peripheral nerves, but not in the central nervous system. This integrin heterodimer has previously been found in perineural fibroblast-like cells and in Schwann cells (SCs), which both assemble a basement membrane but do not form hemidesmosomes. We show here that in SCs, which had formed a myelin sheath, alpha 6 beta 4 was enriched in the proximity of the nucleus, at Ranvier paranodal areas and at Schmitt-Lanterman clefts; alpha 6 beta 4 was also found at the grooved interface between small axons and non-myelinating SCs. Immunoprecipitation of human peripheral nerves, in combination with Western blotting showed that beta 4 is associated with the alpha 6A subunit. Northern blot analysis of human peripheral nerves showed a single beta 4 transcript of 6 kb. Using the reverse transcriptase polymerase chain reaction, we detected two mRNA species, one for the most common (−70, -53) form of beta 4 and the other encoding the (+53) variant of beta 4. Cultured SCs were devoid of alpha 6 beta 4 but expressed alpha 6 beta 1, indicating that SCs lose beta 4 expression when contact with neurons is lost. Thus, resting SCs in contact with axons express alpha 6A in combination with beta 4, irrespective of myelin formation. We suggest that alpha 6 beta 4 expressed in SCs plays a role in peripheral neurogenesis.

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