GENETIC TYPING OF LEUCONOSTOC MESENTEROIDES USING PCR

2020 ◽  
pp. 40-49
Author(s):  
A. Biruk ◽  
Y. Tarashkevich ◽  
N. Furik
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Heterogeneity ◽  
Leuconostoc Mesenteroides ◽  
Genetic Differences ◽  
Bootstrap Support ◽  
Genetic Typing ◽  
Rapd Pcr ◽  
High Level ◽  
Combined Methods

We studied the possibility of using RAPD-PCR with primers: ERIC1R-1, ERIC2-1, BOXA1R, BOXA2R and Rep-PCR with primers P15, P16, XD8, XD9, RAPD-mes, (GTG)5 to identify genetic heterogeneity of 9 strains and 8 isolates of Leuconostoc mesenteroides. Three clusters of cultures with a high level of bootstrap support were identified as a result of phylogenetic analysis obtained when typing Leuconostoc. The obtained results indicate the possibility of revealing genetic differences in the profile of the generated amplicons among Leuconostoc mesenteroides strains using the combined methods of Rep-PCR and RAPD-PCR.

scholarly journals Phylogenetic analysis of the Andean genus Brachycladium Luer (syn. Oreophilus Higgins & Archila) and closely related genera based on nuclear ITS sequencing

Lankesteriana ◽  
2011 ◽  
Vol 11 (3) ◽  
Author(s):  
Mark Wilson ◽  
Lou Jost
Keyword(s):  
Phylogenetic Analysis ◽  
Cryptic Species ◽  
Bootstrap Support ◽  
Its Sequencing ◽  
Morphological Similarity ◽  
Additional Species ◽  
Nuclear Its ◽  
High Level ◽  
Relationship Of ◽  
The Relationship

We previously reported that nrITS sequencing and phylogenetic analysis revealed at least four cryptic species within Brachycladium nummularium (syn. Oreophilus nummularius). Sequencing of additional species in the genus revealed two major clades within Brachycladium, the “nummularium”-complex plus B. stalactites and Luer’s section Amplectentes. Since the relationship of Brachycladium to Andinia had been noted earlier, a number of Andinia species were also included. Two clades were observed, a clade containing A. lappacea, A. pensilis, and A. vestigipetala that was closely related to Brachycladium and a second, more distantly related clade containing A. dalstroemii, A. pogonion, and A. schizopogon. Samples of two additional genera, Masdevalliantha Szlachetko & Margonska and Xenosia Luer, were included in the analysis based upon morphological similarity to Andinia. These two genera formed a clade that was sister to both Brachycladium and Andinia. Only the node subtending clades of all four genera had a high level of bootstrap support, whereas nodes subtending clades of Brachycladium plus Andinia, or Brachycladium alone, had much lower support. If future chloroplast sequencing produces phylogenies congruent with nrITS, this would indicate that Andinia, Brachycladium (syn. Oreophilus), Masdevalliantha, and Xenosia should all be placed in the same genus. 

scholarly journals Significant contribution of the CmeABC Efflux pump in high-level resistance to ciprofloxacin and tetracycline in Campylobacter jejuni and Campylobacter coli clinical isolates

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Saeed Sharifi ◽  
Bita Bakhshi ◽  
Shahin Najar-peerayeh
Keyword(s):  
Gene Expression ◽  
Point Mutation ◽  
Campylobacter Jejuni ◽  
Significant Contribution ◽  
Efflux Pump ◽  
Campylobacter Coli ◽  
Rapd Pcr ◽  
Resistant Strains ◽  
High Level ◽  
Level Resistance

Abstract Background Campylobacter resistance to antimicrobial agents is regarded as a major concern worldwide. The aim of this study was to investigate the expression of the CmeABC efflux pump and the RAPD-PCR pattern in drug-resistant Campylobacter isolates. Methods A total of 283 stool specimens were collected from children under the age of five with diarrhea. The minimum inhibitory concentration (MIC) of tetracycline and ciprofloxacin was determined by broth microdilution method and E-test, respectively. Detection of tetracycline and ciprofloxacin determinants was done by amplification of tetO gene and PCR-sequencing of the gyrA gene. The cmeABC transcriptional expression was analyzed by Real-time (RT)-PCR. Clonal correlation of resistant strains was determined by RAPD-PCR genotyping. Results Out of 283 fecal samples, 20 (7.02%) samples were positive for Campylobacter spp. Analysis of duplex PCR assay of the cadF gene showed that 737 and 461 bp amplicons were corresponding to Campylobacter jejuni and Campylobacter coli, respectively. All of the 17 phenotypically tetracycline-resistant Campylobacter isolates harbored the tetO gene. Also, four phenotypically ciprofloxacin-resistant Campylobacter isolates had a point mutation at codon 257 of the gyrA gene (ACA to ATA; Thr > Ile). High-level expression of the cmeA gene was observed in ciprofloxacin-resistant and high-level tetracycline-resistant Campylobacter isolates, suggesting a positive correlation between the cmeA gene expression level and tetracycline resistance level. Moreover, a statistically significant difference was observed in the cmeA gene expression between ciprofloxacin-resistant and ciprofloxacin-susceptible strains, which signifies the crucial contribution of the efflux pump in conferring multiple drug resistance phenotype among Campylobacter spp. RAPD analysis of Campylobacter isolates exhibited 16 different patterns. Simpsone`s diversity index of RAPD-PCR was calculated as 0.85, showing a high level of homogeneity among the population; however, no clear correlation was detected among tetracycline and/or ciprofloxacin resistant isolates. Conclusion Significant contribution of the CmeABC efflux pump in conferring high-level resistance to tetracycline and ciprofloxacin was observed in C. jejuni and C. coli clinical isolates. The resistant phenotype is suggested to be mediated by CmeABC efflux pumps, the tetO gene, and point mutation of the gyrA gene. Genotyping revealed no clonal correlation among resistant strains, indicating distinct evolution of tetracycline and ciprofloxacin resistant genotypes among the isolates.

Variation in Salmonella Enteritidis RAPD-PCR Patterns May Not Be Due to Genetic Differences

2011 ◽  
Vol 6 (4) ◽  
pp. e48-e49
Author(s):  
Demetrius L Mathis ◽  
Roy D Berghaus ◽  
Margie D Lee ◽  
John J Maurer
Keyword(s):  
Salmonella Enteritidis ◽  
Genetic Differences ◽  
Rapd Pcr

scholarly journals Molecular characterization and phylogenetic analysis of one Omega-gliadin gene from Aegilops speltoidesl

Genetika ◽  
2018 ◽  
Vol 50 (2) ◽  
pp. 503-517 ◽  
Author(s):  
Wanqing Wang ◽  
Ke Wang ◽  
Xi Chen ◽  
Slaven Prodanovic ◽  
Xiaohui Li ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Quality Improvement ◽  
Related Species ◽  
Storage Proteins ◽  
Aegilops Speltoides ◽  
Amino Acid Residues ◽  
Sequence Characterization ◽  
Specific Pcr ◽  
High Level ◽  
Wheat Storage Proteins

Gliadins, as the major components of wheat storage proteins, determine the extensibility properties of dough and have important effects on flour processing quality. Wheat related species carries potential storage protein gene resources for quality improvement. In this study, we isolated and characterized the first complete ?-gliadin gene Omega-AS from Aegilops speltoides L. (2n = 2x = 14, SS) by allelic-specific PCR and investigated its phylogenetic relationships among Triticum and Aegilopsspecies. Molecular structure showed that Omega-AS gene consisted of 1122 bp encoding 373 amino acid residues with deduced molecular mass 41379.21 Da. Omega-AS gene was exceptionally rich in prolines and glutamines with fewer methionine and no cysteine. Sequence characterization and epitope analysis showed that three epitopes QQPIPVQPQQ, TQPQQPTPIQ and IQPQQPFPQQ were absent in Omega-AS gene encoded protein, indicating its potential value for wheat quality improvement with less toxic, or no toxic peptides. Phylogenetic analysis revealed that Omega-AS was closely related to gliadin genes of wheat and related species and its divergence from bread wheat was more recently (less than 1.243 MYA). Heterologous expression showed that Omega-AS gene could successfully express with a high level in E. coli under the control of T7promoter. The transcription expression pattern of Omega-AS gene during grain development detected by qRT-PCR revealed that the highest expression level occurred at 17 days post an thesis.

Morphological evidence for paraphyly of Holopothrips Hood (Thysanoptera: Phlaeothripidae), a Neotropical genus of gall-inducing thrips

2021 ◽  
pp. 1-24
Author(s):  
Mariana F. Lindner ◽  
Augusto Ferrari ◽  
Adriano Cavalleri
Keyword(s):  
Phylogenetic Analysis ◽  
Host Plants ◽  
Morphological Diversity ◽  
Morphological Characters ◽  
Bootstrap Support ◽  
Morphological Evidence ◽  
Diverse Group ◽  
The Matrix ◽  
Internal Relations ◽  
Evolutionary Story

Abstract Holopothrips is a diverse group of thrips associated to galls in the Neotropics, with a variety of host plants and wide morphological diversity. Relationships to other Neotropical groups have been proposed, but are still untested, and the monophyly of the genus remains doubtful. Here, we perform a phylogenetic analysis of Holopothrips, based on morphological characters. A total of 87 species were included in the matrix and eight analyses were carried out, but all of them failed to recover Holopothrips as a monophyletic grouping. Bremer and Bootstrap support values were low, and the topologies varied among all analyses, with uncertain internal relations for the ingroup. These results indicate that the relationships for Holopothrips species, and the proposed related genera, are more complex than previously reported; and morphological characters may not be enough to recover the evolutionary story within this group. We also discuss the influences of different character coding, continuous characters and weighting schemes in our results.

A re-evaluated taxon: Genetic values and morphological characters support the recognition of the Canary Island juniper of the phoenicea group at a specific level

Phytotaxa ◽  
2019 ◽  
Vol 406 (1) ◽  
pp. 64 ◽  
Author(s):  
ANGEL ROMO ◽  
MAŁGORZATA MAZUR ◽  
MONTSERRAT SALVÀ-CATARINEU ◽  
ADAM BORATYŃSKI
Keyword(s):  
Canary Island ◽  
Morphological Traits ◽  
Morphological Characters ◽  
Genetic Differences ◽  
Specific Level ◽  
Data Support ◽  
Juniperus Phoenicea ◽  
High Level

Analyses based on cone, seed and needle characteristics revealed that J. canariensis Guyot in Mathou & Guyot is distinct from both the Circum-Mediterranean J. turbinata and West-Mediterranean J. phoenicea. The genetic differences between these three taxa, which make up the aggregate of J. phoenicea, are found also at a high level. These data support the recognition of the Canarian juniper at the specific level. A key is proposed, in which taxa of the J. phoenicea aggregate can be distinguished on the basis of morphological traits.                The nomenclatural name: Juniperus phoenicea subsp. canariensis, widely employed in the literature, is validly published. Besides we adduce that Juniperus canariensis Knight ex Godron, is not a validly published name, and therefore can not be considered an earlier homonym of J. canariensis Guyot in Mathou & Guyot.

scholarly journals Sequencing, Cloning, and High-Level Expression of the pfp Gene, Encoding a PPi-Dependent Phosphofructokinase from the Extremely Thermophilic EubacteriumDictyoglomus thermophilum

2000 ◽  
Vol 182 (16) ◽  
pp. 4661-4666 ◽  
Author(s):  
Yan-Huai R. Ding ◽  
Ron S. Ronimus ◽  
Hugh W. Morgan
Keyword(s):  
Phylogenetic Analysis ◽  
Cloning And Expression ◽  
High Level Expression ◽  
Gene Encoding ◽  
Thermoproteus Tenax ◽  
High Level ◽  
High Degree ◽  
Dictyoglomus Thermophilum ◽  
Degree Of Similarity

ABSTRACT The sequencing, cloning, and expression of the pfp gene from Dictyoglomus thermophilum, which consists of 1,041 bp and encodes a pyrophosphate-dependent phosphofructokinase, are described. A phylogenetic analysis indicates that the enzyme is closely related to the pyrophosphate-dependent enzyme from Thermoproteus tenax. The recombinant and native enzymes share a high degree of similarity for most properties examined.

Platypus immunoglobulin M and the divergence of the two extant monotreme lineages

2003 ◽  
Vol 25 (1) ◽  
pp. 87 ◽  
Author(s):  
K Belov ◽  
L Hellman
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Common Ancestor ◽  
Variable Region ◽  
Immunoglobulin M ◽  
Last Common Ancestor ◽  
Constant Region ◽  
Sequence Comparisons ◽  
Level Sequence ◽  
High Level

A full-length cDNA clone encoding the platypus (Ornithorynchus anatinus) immunoglobulin M (IgM) heavy chain was isolated from a spleen cDNA library using a short-beaked echidna (Tachyglossus aculeatus) IgM constant region (Cµ) probe. The isolation of platypus IgM shows that O. anatinus, like all other examined jawed vertebrates, express a classical IgM molecule. Amino acid sequence comparisons of the constant regions of IgM reveals a high level sequence conservation between O. anatinus and T. aculeatus sequences (87%), and only approximately 48% identity between O. anatinus and therian Cµ sequences. The variable region of this clone belongs to clan 3, supporting the view that this family is used preferentially, if not exclusively by O. anatinus, as opposed to the use of all three variable region clans by T. aculeatus. Phylogenetic analysis of Cµ sequences supports the traditional Theria hypothesis and suggests that the O. anatinus and T. aculeatus lineages separated from their last common ancestor approximately 21 million years ago.

Sign in / Sign up

Export Citation Format

Share Document