scholarly journals Microsatellite-Based Genotyping, Analysis of Population Structure, Presence of Trichomonas vaginalis Virus (TVV) and Mycoplasma hominis in T. vaginalis Isolates from Southwest of Turkey

2021 ◽  
Author(s):  
Hatice ERTABAKLAR ◽  
Erdoğan MALATYALI ◽  
Elif Pelin ÖZÜN ÖZBAY ◽  
İbrahim YILDIZ ◽  
Mahmut SİNECEN ◽  
...  
Keyword(s):  
Population Structure ◽  
Trichomonas Vaginalis ◽  
Clustering Algorithm ◽  
Mycoplasma Hominis ◽  
Microsatellite Data ◽  
Web Based ◽  
Promising Tool ◽  
Genetic Groups ◽  
Clonal Distribution ◽  
First Time

Background: The present study aimed to determine genetic diversity of Trichomonas vaginalis (T. vaginalis) isolates with microsatellite markers in Turkey (Nov 2015 to 2016) and to create a web-based microsatellite typing (MT) approach for the global interpretation of the data. In addition, the endosymbiosis of Mycoplasma hominis (M. hominis) and T. vaginalis virus (TVV) in the isolates was also examined. Methods: The allele sizes for each locus were calculated and microsatellite types were determined according to the allele profiles. The population structure was examined with Bayesian clustering method. A website (http://mttype.adu.edu.tr) was created for collection and sharing of microsatellite data. Presence of TVV and M. hominis in T. vaginalis isolates were investigated with electrophoresis and PCR. Results: Of 630 vaginal samples T. vaginalis was detected in 30 (4.7%) and those were used for further analysis. The structure produced by a clustering algorithm revealed eight genetic groups. The typing of isolates according to microsatellites revealed 23 different microsatellite types. Three clones were determined among isolates (MT10 16.7%; MT18 10% and MT3 6.7%). The frequency of TVV and M. hominis was 16.6% (n=5) and 20% (n=6), respectively. Conclusion: Presence of three clones among 30 T. vaginalis isolates indicated that microsatellite-based genotyping was efficient to determine the clonal distribution of T. vaginalis isolates. Therefore, a promising tool might be developed further and adapted to the studies dealing with molecular epidemiology of T. vaginalis. Microsatellite data from forthcoming studies will be deposited and presented on the website. In addition, we also presented the frequency of two endosymbionts in T. vaginalis isolates for the first time in Turkey

scholarly journals PSV-16 Infrared thermography technology as a promising tool for assessing temperament of water buffaloes

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 220-221
Author(s):  
Caroline L Francisco ◽  
André M Castilhos ◽  
Daiane C Marques da Silva ◽  
Fabiola Martinez da Silva ◽  
Aline S Aranha ◽  
...  
Keyword(s):  
Infrared Thermography ◽  
Fixed Effects ◽  
Thermal Imager ◽  
Initial Body Weight ◽  
Water Buffaloes ◽  
Promising Tool ◽  
Genetic Groups ◽  
Body Regions ◽  
The Mean ◽  
Positive Correlations

Abstract This study evaluated the use of the infrared thermography (IT) as a tool to identify the temperament of 75 non-castrated water buffaloes (390±32 days of age; 310±61.27 kg of initial body weight) of 3 genetic groups (GG:Jafarabadi, Mediterranean, and Murrah; n = 25 for each GG). The animals were classified for temperament through the temperament score (TSc) obtained by the mean of the sum of the scores of the time of entry into the squeeze chute (1 to 5: 1=greater time spent for entry; 5=less time spent for entry) and the exit velocity score (1 to 5: 1=lower speed; 5=higher speed) calculated after the period of adaptation to the feedlot (d0). The animals were categorized into adequate (ADQ; TSc≤3) or excitable (EXC; TSc >3) temperaments. The rectal temperature was measured and IT images were obtained (Testo 882 Thermal Imager, Testo, Inc, Germany) from regions of the chest, eye, snout, cheek, foreleg (left side), ribs, hind legs, rear area (left side), and scrotum on d0. Data were analyzed using MIXED procedure in SAS, considering the GG, temperament, and the resulting interaction as fixed effects. Correlation was analyzed using the CORR procedure of SAS. There were no effects of interactions (P ≥ 0.14). ADQ animals showed lower rectal (P = 0.02) and ribs (P = 0.05) temperatures than EXC animals (Table1). Tendencies for temperament effect were detected for chest (P = 0.06) and rear area (P = 0.07). There was no effect of temperament for other variables (P = 0.19). Positive correlations were verified between the TSc and rectal (r=0.36; P < 0.01), chest (r=0.35; P < 0.01), and rear area (r=0.33; P < 0.01) temperatures. Tendency for a positive correlation was detected between TSc and scrotum (r=0.23; P = 0.07). In conclusion, the temperament causes changes in the temperature of some body regions suggesting the IT technology may be a promising tool for assessing the temperament of water buffaloes. Supported by FAPESP (#2018/25939-1; #2014/05473-7).

scholarly journals Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication

2021 ◽  
Vol 134 (5) ◽  
pp. 1343-1362
Author(s):  
Alex C. Ogbonna ◽  
Luciano Rogerio Braatz de Andrade ◽  
Lukas A. Mueller ◽  
Eder Jorge de Oliveira ◽  
Guillaume J. Bauchet
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Manihot Esculenta ◽  
Ex Situ ◽  
Germplasm Bank ◽  
Effective Population ◽  
Manihot Esculenta Crantz ◽  
Genetic Groups ◽  
Population Structure Analysis ◽  
Modern Breeding

Abstract Key message Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation. Abstract Cassava (Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonian region. In this study, 3354 cassava landraces and modern breeding lines from the Embrapa Cassava Germplasm Bank (CGB) were characterized. All individuals were subjected to genotyping-by-sequencing (GBS), identifying 27,045 single-nucleotide polymorphisms (SNPs). Identity-by-state and population structure analyses revealed a unique set of 1536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, a density of 1300–4700 SNP markers were selected for large-effect quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity $$({H}_{o})$$ ( H o ) , effective population size estimate $$\widehat{{(N}_{e}}$$ ( N e ^ ) and polymorphism information content (PIC). Selection footprints and introgressions of M. glaziovii were detected. Spatial population structure analysis revealed five ancestral populations related to distinct Brazilian ecoregions. Estimation of historical relationships among identified populations suggests an early population split from Amazonian to Atlantic forest and Caatinga ecoregions and active gene flows. This study provides a thorough genetic characterization of ex situ germplasm resources from cassava’s center of origin, South America, with results shedding light on Brazilian cassava characteristics and its biogeographical landscape. These findings support and facilitate the use of genetic resources in modern breeding programs including implementation of association mapping and genomic selection strategies.

scholarly journals Genetic and Antigenic Characterization of Avian Avulavirus Type 6 (AAvV-6) Circulating in Canadian Wild Birds (2005–2017)

Viruses ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 543
Author(s):  
Tamiko Hisanaga ◽  
Catherine Soos ◽  
Nicola Lewis ◽  
Oliver Lung ◽  
Matthew Suderman ◽  
...  
Keyword(s):  
Clinical Symptoms ◽  
Fusion Gene ◽  
Full Genome ◽  
Genome Sequences ◽  
Viral Shedding ◽  
Genetic Groups ◽  
Antigenic Characterization ◽  
Specific Pathogen ◽  
First Time

We describe for the first time the genetic and antigenic characterization of 18 avian avulavirus type-6 viruses (AAvV-6) that were isolated from wild waterfowl in the Americas over the span of 12 years. Only one of the AAvV-6 viruses isolated failed to hemagglutinate chicken red blood cells. We were able to obtain full genome sequences of 16 and 2 fusion gene sequences from the remaining 2 isolates. This is more than double the number of full genome sequences available at the NCBI database. These AAvV-6 viruses phylogenetically grouped into the 2 existing AAvV-6 genotype subgroups indicating the existence of an intercontinental epidemiological link with other AAvV-6 viruses isolated from migratory waterfowl from different Eurasian countries. Antigenic maps made using HI assay data for these isolates showed that the two genetic groups were also antigenically distinct. An isolate representing each genotype was inoculated in specific pathogen free (SPF) chickens, however, no clinical symptoms were observed. A duplex fusion gene based real-time assay for the detection and genotyping of AAvV-6 to genotype 1 and 2 was developed. Using the developed assay, the viral shedding pattern in the infected chickens was examined. The chickens infected with both genotypes were able to shed the virus orally for about a week, however, no significant cloacal shedding was detected in chickens of both groups. Chickens in both groups developed detectable levels of anti-hemagglutinin antibodies 7 days after infection.

Empirical Evaluation of Genetic Clustering Methods Using Multilocus Genotypes From 20 Chicken Breeds

Genetics ◽  
2001 ◽  
Vol 159 (2) ◽  
pp. 699-713
Author(s):  
Noah A Rosenberg ◽  
Terry Burke ◽  
Kari Elo ◽  
Marcus W Feldman ◽  
Paul J Freidlin ◽  
...  
Keyword(s):  
Cluster Analysis ◽  
Population Structure ◽  
Clustering Algorithm ◽  
Empirical Evaluation ◽  
Unknown Origin ◽  
Clustering Methods ◽  
Genetic Cluster ◽  
Data Set ◽  
Multilocus Genotypes ◽  
Chicken Breeds

Abstract We tested the utility of genetic cluster analysis in ascertaining population structure of a large data set for which population structure was previously known. Each of 600 individuals representing 20 distinct chicken breeds was genotyped for 27 microsatellite loci, and individual multilocus genotypes were used to infer genetic clusters. Individuals from each breed were inferred to belong mostly to the same cluster. The clustering success rate, measuring the fraction of individuals that were properly inferred to belong to their correct breeds, was consistently ~98%. When markers of highest expected heterozygosity were used, genotypes that included at least 8–10 highly variable markers from among the 27 markers genotyped also achieved >95% clustering success. When 12–15 highly variable markers and only 15–20 of the 30 individuals per breed were used, clustering success was at least 90%. We suggest that in species for which population structure is of interest, databases of multilocus genotypes at highly variable markers should be compiled. These genotypes could then be used as training samples for genetic cluster analysis and to facilitate assignments of individuals of unknown origin to populations. The clustering algorithm has potential applications in defining the within-species genetic units that are useful in problems of conservation.

Association between Participation in an Intensive Longitudinal Assessment Program and Performance on a Cognitive Examination in the Maintenance of Certification in Anesthesiology Program®

2016 ◽  
Vol 125 (5) ◽  
pp. 1046-1055 ◽  
Author(s):  
Huaping Sun ◽  
Yan Zhou ◽  
Deborah J. Culley ◽  
Cynthia A. Lien ◽  
Ann E. Harman ◽  
...  
Keyword(s):  
North Carolina ◽  
Learning Resources ◽  
Longitudinal Assessment ◽  
Immediate Feedback ◽  
High Stakes ◽  
Web Based ◽  
Maintenance Of Certification ◽  
Improved Performance ◽  
And Performance ◽  
First Time

Abstract Background As part of the Maintenance of Certification in Anesthesiology Program® (MOCA®), the American Board of Anesthesiology (Raleigh, North Carolina) developed the MOCA Minute program, a web-based intensive longitudinal assessment involving weekly questions with immediate feedback and links to learning resources. This observational study tested the hypothesis that individuals who participate in the MOCA Minute program perform better on the MOCA Cognitive Examination (CE) compared with those who do not participate. Methods Two separate cohorts of individuals eligible for July 2014 and January 2015 CEs were invited to participate in this pilot. The CE scores for each cohort were compared between those who did and did not participate, controlling for the factors known to affect performance. For the first cohort, examination performances for topics covered and not covered by the MOCA Minute were analyzed separately. Results Six hundred sixteen diplomates in July 2014 and 684 diplomates in January 2015 took the CE for the first time. In multiple regression analysis, those actively participating scored 9.9 points (95% CI, 0.8 to 18.9) and 9.3 points (95% CI, 2.3 to 16.3) higher when compared with those not enrolled, respectively. Compared to the group that did not enroll in MOCA Minute, those who enrolled but did not actively participate demonstrated no improvement in scores. MOCA Minute participation was associated with improvement in both questions covering topics included the MOCA Minute and questions not covering these topics. Conclusions This analysis provides evidence that voluntary active participation in a program featuring frequent knowledge assessments accompanied by targeted learning resources is associated with improved performance on a high-stakes CE.

scholarly journals Genetic Diversity and Population Structure of Brachiaria (syn. Urochloa) Ecotypes from Uganda

Agronomy ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1193
Author(s):  
Clementine Namazzi ◽  
Julius Pyton Sserumaga ◽  
Swidiq Mugerwa ◽  
Martina Kyalo ◽  
Collins Mutai ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Crop Production ◽  
Clustering Algorithm ◽  
Principal Component ◽  
Model Based Clustering ◽  
High Gene ◽  
Nj Tree ◽  
Improvement Programs ◽  
The Tropics

Brachiaria (syn. Urochloa) grass is an important tropical forage of African origin that supports millions of livestock and wildlife in the tropics. Overgrazing, conversion of grasslands for crop production and non-agricultural uses, and the introduction of improved forages have threatened the natural diversity of Brachiaria grass in Uganda. This study established a national collection of Brachiaria ecotypes in Uganda and analyzed them for genetic diversity and population structure using 24 simple sequence repeats (SSR) markers. These markers had a high discriminating ability with an average polymorphism information content (PIC) of 0.89 and detected 584 alleles in 99 ecotypes. Analysis of molecular variance revealed a high within populations variance (98%) indicating a high gene exchange or low genetic differentiation (PhiPT = 00.016) among the ecotype populations. The Bayesian model based clustering algorithm showed three allelic pools in Ugandan ecotypes. The principal component analysis (PCA) of ecotypes, and Neighbor-joining (NJ) tree of ecotypes and six commercial cultivars showed three main groups with variable membership coefficients. About 95% of ecotype pairs had Rogers’ genetic distance above 0.75, suggesting most of them were distantly related. This study confirms the high value of these ecotypes in Brachiaria grass conservation and improvement programs in Uganda and elsewhere.

scholarly journals Nearest-Neighbour-Induced Isolation Similarity and Its Impact on Density-Based Clustering

2019 ◽  
Vol 33 ◽  
pp. 4755-4762 ◽  
Author(s):  
Xiaoyu Qin ◽  
Kai Ming Ting ◽  
Ye Zhu ◽  
Vincent CS Lee
Keyword(s):  
Clustering Algorithm ◽  
Distance Measure ◽  
Nearest Neighbour ◽  
Density Peak ◽  
Density Based Clustering ◽  
New Type ◽  
Density Peak Clustering ◽  
The Impact ◽  
First Time ◽  
Tree Method

A recent proposal of data dependent similarity called Isolation Kernel/Similarity has enabled SVM to produce better classification accuracy. We identify shortcomings of using a tree method to implement Isolation Similarity; and propose a nearest neighbour method instead. We formally prove the characteristic of Isolation Similarity with the use of the proposed method. The impact of Isolation Similarity on densitybased clustering is studied here. We show for the first time that the clustering performance of the classic density-based clustering algorithm DBSCAN can be significantly uplifted to surpass that of the recent density-peak clustering algorithm DP. This is achieved by simply replacing the distance measure with the proposed nearest-neighbour-induced Isolation Similarity in DBSCAN, leaving the rest of the procedure unchanged. A new type of clusters called mass-connected clusters is formally defined. We show that DBSCAN, which detects density-connected clusters, becomes one which detects mass-connected clusters, when the distance measure is replaced with the proposed similarity. We also provide the condition under which mass-connected clusters can be detected, while density-connected clusters cannot.

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