scholarly journals A New PCR-Based Species Genotyping Differentiation Approach in Entamoeaba

2019 ◽  
Vol 16 (3) ◽  
pp. 491-508
Author(s):  
Dalia Abuljadayel ◽  
Ahmed Atef ◽  
Mohammed Al-Matary ◽  
Sherif Edris ◽  
Khalid M. Al-Ghamdi ◽  
...  
Keyword(s):  
Entamoeba Histolytica ◽  
Selection Criteria ◽  
Good Choice ◽  
Species Differentiation ◽  
Parasite Diversity ◽  
High Similarity ◽  
Banding Patterns ◽  
Strain Differentiation ◽  
New Approach ◽  
Primer Sets

The most commonly used approach for Entamoeba species differentiation up to date is the tRNA-linked STR regions of the parasite’s genome. In the present study, a new reliable, fast and easy molecular tool for species differentiation was developed. DNA was isolated from fecal samples collected from infected subjects with either Entamoeba histolytica (EH) or Entamoeba disper (ED) in Saudi Arabia. Two types of primer sets were compared in which the first targeted tRNA-linked STR regions, while the second was designed after multiple contig alignment of the two genomes using NUCmer program in aligned areas with high similarity (~90%) and difference between of ~90 bp. The selection criteria secures that designed primers should pair with both EH and ED contig sequences at homologous regions of 200-500 bp of both species except for the presence of indels that result in the recovery of amplicons of two species with different sizes. Banding patterns in the tRNA-linked STR region resulted in the occurrence of several common amplicons. We speculate that primers mismatch with regions other than the specified STR arrays of Entamoeba histolytica or Entamoeba disper with organisms other than Entamoeba existed in the fecal sample. However, the STR-based approach looked very useful in studying strain differentiation and parasite diversity. The results for the new approach complemented those of the STR-based approach, except that the latter failed to detect coinfected subjects. The new approach proved to be useful at the species level, while the tRNA-linked STR approach can still be a good choice for strain differentiation.

scholarly journals Hairs of wild Felis silvestris silvestris and domestic Felis catus – are they distinctive after all? (Carnivora: Felidae)

2021 ◽  
Vol 51 (1) ◽  
pp. 65-79
Author(s):  
Lisa Lehmann ◽  
Clara Stefen
Keyword(s):  
Hair Shaft ◽  
Felis Catus ◽  
Species Differentiation ◽  
Hair Length ◽  
Felis Silvestris ◽  
Domestic Cats ◽  
Banding Patterns ◽  
Felis Silvestris Silvestris ◽  
Wild Cats ◽  
First Time

This study addressed the question whether it is possible to clearly differentiate between wild and tabby domestic cats on the basis of hairs (guard hairs in particular). The colour banding pattern of individual hairs is studied in this context for the first time. Also, hair length and width, as well as parameters of the hair cuticle were checked for differences, as it is well known that wild cats have long hairs and a fine, silky fur. Several banding patterns were observed, some shared between both cat forms, but with different frequencies. But this is not enough for species differentiation and more specimens need to be studied to get a better idea of the variation in this trait. The cuticle pattern even in the same region of the hairs (medium and shield-free part of the hair shaft) varies considerably and statistically significant differences were found only for few measured parameters: hair length, hair width and scale perimeter. Nevertheless, even most of them are not sufficient to determine wild or domestic cats. However, as expected, the hairs of wild cats are statistically significantly longer than those of tabby domestic cats, and hairs longer than 50 mm can be clearly attributed to wild cats.

scholarly journals Outbreak of Glomerulonephritis byStreptococcus zooepidemicusSzPHV5 type, in Monte Santo de Minas, Minas Gerais, Brazil

2018 ◽  
Author(s):  
Rosângela S.L.A. Torres ◽  
Talita Z. Santos ◽  
Andre F. L. Bernardes ◽  
Patricia A. Soares ◽  
Ana C. C. Soares ◽  
...  
Keyword(s):  
Hypervariable Region ◽  
Streptococcus Zooepidemicus ◽  
Food Handlers ◽  
High Similarity ◽  
Milk Supply ◽  
Banding Patterns ◽  
Zoonotic Pathogen ◽  
Life Threatening ◽  
Post Streptococcal Glomerulonephritis ◽  
The Town

ABSTRACTStreptococcus zooepidemicusis an emerging and opportunistic zoonotic pathogen, which playsan important role in the development of severe and life-threatening diseases and potentially capable of triggering large glomerulonephritis outbreaks. Between December 2012 and February 2013, 175 cases of glomerulonephritis were confirmed in the town of Monte Santo de Minas / MG / Brazil. During the outbreak, 19 isolates ofS. zooepidemicuswere recovered: one from ice cream, two from the oropharynx of food handlers and 16 from patients affected by acute post streptococcal glomerulonephritis (APSGN). AllS. zooepidemicusinvolved in the outbreak amplified the same sequence of the hypervariable region of the SzP protein (SzPHV5) and presented indistinguishable banding patterns with high similarity (> 99%) by rep-PCR technique. Inspection programs on the milk supply chain should be strengthened and continuously encouraged so that consumers’ health is preserved.

scholarly journals Touchdown Enzyme Time Release-PCR for Detection and Identification of Chlamydia trachomatis, C. pneumoniae, and C. psittaci Using the 16S and 16S-23S Spacer rRNA Genes

2000 ◽  
Vol 38 (3) ◽  
pp. 1085-1093 ◽  
Author(s):  
Guillermo Madico ◽  
Thomas C. Quinn ◽  
Jens Boman ◽  
Charlotte A. Gaydos
Keyword(s):  
Chlamydia Trachomatis ◽  
Dna Sequences ◽  
Chlamydia Pneumoniae ◽  
Chlamydia Psittaci ◽  
Rrna Genes ◽  
Clinical Samples ◽  
Species Differentiation ◽  
Analytical Sensitivity ◽  
Variable Regions ◽  
Primer Sets

Three touchdown enzyme time release (TETR)-PCR assays were used to amplify different DNA sequences in the variable regions of the 16S and 16S-23S spacer rRNA genes specific for Chlamydia trachomatis, Chlamydia pneumoniae, andChlamydia psittaci as improved tests for sensitive diagnosis and rapid species differentiation. The TETR-PCR protocol used 60 cycles of amplification, which provided improved analytical sensitivity (0.004 to 0.063 inclusion-forming unit ofChlamydia species per PCR). The sensitivity of TETR-PCR with primer set CTR 70-CTR 71 was 96.7%, and the specificity was 99.6%, compared to those of the AMPLICOR PCR for the detection ofC. trachomatis in vaginal swab samples. TETR-PCR forC. pneumoniae with primer set CPN 90-CPN 91 was 90% sensitive and 93.3% specific compared with a nested PCR with primer set CP1/2-CPC/D for clinical respiratory samples. TETR-PCR for C. psittaci with primer set CPS 100-CPS 101 showed substantial agreement with cell culturing (κ, 0.78) for animal tissue samples. Primer sets were then combined into a single multiplex TETR-PCR test. The respective 315-, 195-, and 111-bp DNA target products were precisely amplified when DNA from each of the respectiveChlamydia species or combinations of them was used. Multiplex chlamydia TETR-PCR correctly identified one strain of each of the 15 serovars of C. trachomatis, 22 isolates of C. pneumoniae, and 20 isolates of C. psittaci. The primer sets were specific for each species. No target products were amplified when DNA from C. pecorum or a variety of other microorganisms was tested for specificity. TETR-PCR with primers selected for specific sequences in the 16S and 16S-23S spacer rRNA genes is a valuable test that could be used either with individual primers or in a multiplex assay for the identification and differentiation of Chlamydia species from culture isolates or for the detection of chlamydiae in clinical samples.

Species differentiation in Axelrod’s model

2019 ◽  
Vol 30 (08) ◽  
pp. 1950064 ◽  
Author(s):  
Sandro M. Reia ◽  
Gustavo D. M. Madeira ◽  
João P. Fiorelli ◽  
Ubiraci P. C. Neves
Keyword(s):  
Genetic Information ◽  
Order Parameter ◽  
Distinct Species ◽  
Species Differentiation ◽  
Similar Species ◽  
New Approach ◽  
Predominant Species ◽  
A Genome ◽  
Separation Degree ◽  
Genome Distance

We have proposed a new approach for Axelrod’s model to describe newly recognized mechanisms of speciation based on the interbreedings between genetically similar species. By tracking the propagation of genetic information through the network, our modeling suggests that species (agents) that once were able to exchange genetic information tend to evolve to a predominant species or even differentiate into distinct species. Furthermore, a genome distance measurement (separation degree) is here defined and shown to capture the phase transition of the model, thus working as an alternative and computationally less costly order parameter.

scholarly journals Species differentiation of thermotolerant Campylobacters based on distinctive banding patterns obtained by multiplex PCR

2016 ◽  
Vol 33 (No. 1) ◽  
pp. 27-31
Author(s):  
L. Vondráková ◽  
S. Purkrtová ◽  
J. Pázlarová ◽  
K. Demnerová
Keyword(s):  
Multiplex Pcr ◽  
Species Differentiation ◽  
Banding Patterns

scholarly journals Simple Sequence Repeat (SSR) Variation in a Collection of Malus Species and Hybrids

HortScience ◽  
1997 ◽  
Vol 32 (3) ◽  
pp. 440C-440 ◽  
Author(s):  
Stan C. Hokanson ◽  
Amy K. Szewc-McFadden ◽  
Warren F. Lamboy ◽  
James R. McFerson
Keyword(s):  
Genetic Variation ◽  
Simple Sequence Repeat ◽  
Plant Genetic Resources ◽  
Sequence Repeat ◽  
Discrimination Power ◽  
Banding Patterns ◽  
Germplasm Collections ◽  
Duplication Events ◽  
Primer Sets ◽  
Simple Sequence

A diverse collection of 133 Malus species and hybrids from the USDA Plant Genetic Resources Unit's core subset collection was screened with five simple sequence repeat (SSR) primer pairs in order to determine genetic identities and overall levels of genetic variation. The number of amplification products (alleles) per locus (primer pair) in this collection ranged from 6 to 39, with some genotypes showing complex banding patterns of up to four products per locus, suggesting that duplication events may have occurred within the genome. Five primer sets unequivocally differentiated all but 10 pairs of genotypes in the collection, with seven of these 10 being pairs of the same species. Within three of the species holdings surveyed, M. honanensis, M. sargentii, and M. sikkimensis, no genetic variation was revealed with the SSR markers. The discrimination power for the combined loci in this collection was nearly one, which indicates that the likelihood of two genetically different accessions sharing the same alleles at all the loci included in this study would be nearly impossible. Coupled with results from a previous survey of M. × domestica accessions, this finding suggests that with five SSR primer pairs, the majority of the Malus holdings could be assigned a unique fingerprint identity. The average direct count heterozygosity over all loci was 0.620, ranging in value from 0.293 to 0.871 over individual loci. These heterozygosity counts will be compared with a survey of naturally occurring M. sieversii to determine whether current repository holdings are representative of the overall levels of diversity occurring in Malus. Information generated with this study, coupled with passport and horticultural data will inform curatorial decisions regarding deaccessioning of duplicate holdings and plans for future germplasm collections.

Etude de la structure isoenzymatique de quelques enzymes de variétés de Vitis vinifera et de porte-greffes. Application a la détermination biochimique de l'affinité greffon-variété

OENO One ◽  
1986 ◽  
Vol 20 (1) ◽  
pp. 1
Author(s):  
Antón Masa
Keyword(s):  
Vitis Vinifera ◽  
Gel Electrophoresis ◽  
Polyacrylamide Gel Electrophoresis ◽  
Biochemical Method ◽  
Alkaline Phosphatases ◽  
Banding Patterns ◽  
New Approach ◽  
Electrophoretic Mobilities ◽  
Valid Evidence

<p style="text-align: justify;">Dans le but de compléter la méthode biochimique de détermination de l'affinité entre <em>Vitis vinifera</em> et porte-greffe, on étudie, par électrophorèse sur gel de polyacrylamide, le profil isoenzymatique de quatre systèmes enzymatiques (phosphatases acide et alcaline, peroxydase et estérase) chez cinq variétés et six porte-greffes. A partir des mobilités électrophorétiques relatives le calcul des valeurs des coefficients d'affinité permet d'établir, pour chaque enzyme, une relation d'affinité ou de non-affinité des diverses associations <em>vinifera</em>-porte-greffes. Ces résultats sont comparés à ceux obtenus à partir des dosages de protéines totales. Les phosphatases acide et alcaline apparaissent les plus adaptées pour la détermination de l'affinité variété-porte-greffe.</p><p style="text-align: justify;">+++</p><p style="text-align: justify;">ln order to complete the biochemical method for determination of scion roots-stock affinity in grape a new approach is proposed such as the study and comparison of isoenzymatic structure of some scions and rootstocks enzymes. Acidic and alkaline phosphatases, peroxidase and esterase of five <em>Vitis vinifera</em> and six rootstocks were analysed by polyacrylamide gel electrophoresis. Relative electrophoretic mobilities of the different isoenzymatic bands were calculated. After comparing the zymogram banding patterns it was concluded that this new approach was valid. Evidence occured that acidic and alkaline phosphatases were the most useful for determining the scion-rootstock affinity. Results were in agreement with those previously obtained according to protein determinations.</p>

Pruning High-Similarity Clusters to Optimize Data Diversity when Building Ensemble Classifiers

2019 ◽  
Vol 18 (04) ◽  
pp. 1950027
Author(s):  
Sam Fletcher ◽  
Brijesh Verma
Keyword(s):  
State Of The Art ◽  
Computation Time ◽  
Ensemble Classifier ◽  
Classification Error ◽  
Ensemble Classifiers ◽  
High Similarity ◽  
New Approach ◽  
The Past ◽  
Multiple Clusterings ◽  
Benchmark Datasets

Diversity is a key component for building a successful ensemble classifier. One approach to diversifying the base classifiers in an ensemble classifier is to diversify the data they are trained on. While sampling approaches such as bagging have been used for this task in the past, we argue that since they maintain the global distribution, they do not create diversity. Instead, we make a principled argument for the use of [Formula: see text]-means clustering to create diversity. Expanding on previous work, we observe that when creating multiple clusterings with multiple [Formula: see text] values, there is a risk of different clusterings discovering the same clusters, which would in turn train the same base classifiers. This would bias the ensemble voting process. We propose a new approach that uses the Jaccard Index to detect and remove similar clusters before training the base classifiers, not only saving computation time, but also reducing classification error by removing repeated votes. We empirically demonstrate the effectiveness of the proposed approach compared to the state of the art on 19 UCI benchmark datasets.

scholarly journals Variable Numbers of TTC Repeats inMycobacterium leprae DNA from Leprosy Patients and Use in Strain Differentiation

2000 ◽  
Vol 38 (12) ◽  
pp. 4535-4538 ◽  
Author(s):  
Yoo-Chul Shin ◽  
Hyejon Lee ◽  
Hyeyoung Lee ◽  
Gerald P. Walsh ◽  
Joo-Deuk Kim ◽  
...  
Keyword(s):  
Mycobacterium Leprae ◽  
Dna Repeats ◽  
Epidemiological Investigation ◽  
Sequence Database ◽  
Repeat Region ◽  
Strain Differentiation ◽  
Genome Sequence Database ◽  
Leprosy Patients ◽  
Pcr Products ◽  
Primer Sets

Strain differentiation of Mycobacterium leprae would be of great value for epidemiological investigation to identify the infectious sources of leprosy, to understand transmission patterns, and to distinguish between relapse and reinfection. From the M. leprae genome sequence database, TTC DNA repeats were identified. Primer sets designed to amplify the region flanking TTC repeats revealed PCR products of different sizes, indicating that the number of repeats at each locus may be variable among M. lepraestrains. The TTC repeats were not found in Mycobacterium tuberculosis, Mycobacterium avium,Mycobacterium marinum, or human tissues, which indicated their specificity to M. leprae. Sequence analysis of the TTC repeat region in each of the M. leprae strains showed a variation of 10 to 37 repeats. In the M. leprae strains of 34 multibacillary patients at Cebu, Philippines, M. lepraewith 24 and 25 TTC repeats was most common, and this was followed by strains with 14, 15, 20, 21, and 28 repeats. This study thus indicates that there are variable numbers of TTC repeats in a noncoding region ofM. leprae strains and that the TTC region may be useful for strain differentiation for epidemiological investigations of leprosy.

scholarly journals Microbial community structure in hadal sediments: high similarity along trench axes and strong changes along redox gradients

2021 ◽  
Author(s):  
Clemens Schauberger ◽  
Ronnie N. Glud ◽  
Bela Hausmann ◽  
Blandine Trouche ◽  
Lois Maignien ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Ecological Factors ◽  
Sediment Surface ◽  
Rrna Gene ◽  
Organic Carbon Content ◽  
High Similarity ◽  
Redox Stratification ◽  
Potential Factors ◽  
Primer Sets ◽  
Biogeochemical Parameters

AbstractHadal trench sediments are hotspots of biogeochemical activity in the deep sea, but the biogeochemical and ecological factors that shape benthic hadal microbial communities remain unknown. Here, we sampled ten hadal sites from two trench regions with a vertical resolution of down to 1 cm. We sequenced 16S rRNA gene amplicons using universal and archaea-specific primer sets and compared the results to biogeochemical parameters. Despite bathymetric and depositional heterogeneity we found a high similarity of microbial communities within each of the two trench axes, while composition at the phylum level varied strongly with sediment depth in conjunction with the redox stratification into oxic, nitrogenous, and ferruginous zones. As a result, communities of a given sediment horizon were more similar to each other across a distance of hundreds of kilometers within each trench, than to those of adjacent horizons from the same sites separated only by centimeters. Total organic carbon content statistically only explained a small part of the variation within and between trenches, and did not explain the community differences observed between the hadal and adjacent shallower sites. Anaerobic taxa increased in abundance at the top of the ferruginous zone, seeded by organisms deposited at the sediment surface and surviving burial through the upper redox zones. While an influence of other potential factors such as geographic isolation, hydrostatic pressure, and non-steady state depositional regimes could not be discerned, redox stratification and diagenesis appear to be the main selective forces that structure community composition in hadal sediments.

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