scholarly journals Molecular epidemiology of Paracoccidiodes spp. recovered from patients with paracoccidioidomycosis in a teaching hospital from Minas Gerais State of Brazil

2021 ◽  
Vol 15 (11) ◽  
pp. e0009956
Author(s):  
Juliana Andrade-Silva ◽  
Leonardo Euripedes Andrade-Silva ◽  
Hugo Costa Paes ◽  
Lucas Alves ◽  
Adair Rosa ◽  
...  
Keyword(s):  
Geographical Area ◽  
Geographic Origin ◽  
Intraspecific Variability ◽  
Molecular Profile ◽  
Species Differentiation ◽  
Clinical Form ◽  
Exon 2 ◽  
Southeast Region ◽  
Minas Gerais State ◽  
Polymorphism Rate

Introduction Paracoccidioidomycosis (PCM) is caused by several species of the Paracoccidioides genus which can be differentiated by interspecific genetic variations, morphology and geographic distribution. Intraspecific variability correlation with clinical and epidemiological aspects of these species still remains unclear. This study aimed to sequence the loci GP43, exon 2 and ARF of 23 clinical isolates of Paracoccidioides spp. from patients in the Southeast Region of Brazil. Methodology and main findings GenBank was used to compare the present (23) with previous described sequences (151) that included ARF and GP43. It was identified a high polymorphism rate among the 23 isolates in comparison to the other 151. Among the isolates, 22 (95,66%) were S1/P. brasiliensis and 1 (4,34%) was identified as PS2/P. americana. A total of 45 haplotypes were found as follows: 19 from S1/P. brasiliensis (13 from the present study), 15 from P. lutzii, 6 from PS2/P. americana (1 from the present study), 3 from PS3/P. restrepiensis and 2 from PS4/P. venezuelensis. Moreover, exclusive haplotypes according to clinical origin and geographical area were found. S1/P. brasiliensis (HD = 0,655 and K = 4,613) and P. lutzii (HD = 0,649 and K = 2,906) presented the highest rate of polymorphism among all species, from which 12 isolates of the present study were clustered within S1b/P. brasiliensis. The GP43 locus showed a higher variability and was found to be the main reason for the species differentiation. Conclusions The results herein decribed show a high intraspecific genetic variability among S1/P. brasiliensis isolates and confirm the predominance of this species in the Southeast region of Brazil. The finding of exclusive haplotypes according to clinical origin and geographical area would suggest correlation between the molecular profile with the clinical form and geographic origin of patients with PCM.

scholarly journals Prevalence of systemic lupus erythematosus in Spain: higher than previously reported in other countries?

Rheumatology ◽  
2020 ◽  
Vol 59 (9) ◽  
pp. 2556-2562 ◽  
Author(s):  
Raúl Cortés Verdú ◽  
José M Pego-Reigosa ◽  
Daniel Seoane-Mato ◽  
Mercedes Morcillo Valle ◽  
Deseada Palma Sánchez ◽  
...  
Keyword(s):  
Lupus Erythematosus ◽  
Adult Population ◽  
Geographical Area ◽  
Geographic Origin ◽  
The United States ◽  
Epidemiological Studies ◽  
Population Based ◽  
Cross Sectional Study ◽  
Medical Visit ◽  
Cross Sectional

Abstract Objectives Prevalence of SLE varies among studies, being influenced by study design, geographical area and ethnicity. Data about the prevalence of SLE in Spain are scarce. In the EPISER2016 study, promoted by the Spanish Society of Rheumatology, the prevalence estimate of SLE in the general adult population in Spain has been updated and its association with sociodemographic, anthropometric and lifestyle variables has been explored. Methods Population-based multicentre cross-sectional study, with multistage stratified and cluster random sampling. Participants were contacted by telephone to carry out a questionnaire for the screening of SLE. Investigating rheumatologists evaluated positive results (review of medical records and/or telephone interview, with medical visit if needed) to confirm the diagnosis. To calculate the prevalence and its 95% CI, the sample design was taken into account and weighing was calculated considering age, sex and geographic origin. Multivariate logistic regression models were defined to analyse which sociodemographic, anthropometric and lifestyle variables included in the telephone questionnaire were associated with the presence of SLE. Results 4916 subjects aged 20 years or over were included. 16.52% (812/4916) had a positive screening result for SLE. 12 cases of SLE were detected. The estimated prevalence was 0.21% (95% CI: 0.11, 0.40). SLE was more prevalent in the rural municipalities, with an odds ratio (OR) = 4.041 (95% CI: 1.216, 13.424). Conclusion The estimated prevalence of SLE in Spain is higher than that described in most international epidemiological studies, but lower than that observed in ethnic minorities in the United States or the United Kingdom.

Intraspecific variability of morphological characters in the species-rich deep-sea genus Acantholaimus Allgén, 1933 (Nematoda: Chromadoridae)

Nematology ◽  
2016 ◽  
Vol 18 (4) ◽  
pp. 455-473 ◽  
Author(s):  
Dmitry M. Miljutin ◽  
Maria A. Miljutina
Keyword(s):  
Deep Sea ◽  
Intraspecific Variability ◽  
Morphological Characters ◽  
Molecular Data ◽  
Species Discrimination ◽  
Species Differentiation ◽  
Lateral Field ◽  
Operational Taxonomic Units ◽  
General Arrangement ◽  
Taxonomic Approach

Acantholaimusis a species-rich genus of deep-sea nematodes, often with dozens of species found at the same locality but each represented by single or few individuals. Species discrimination by morphological characters in this genus is therefore often difficult due to transitional forms that may be referred to several species because of lack of data on intraspecific variability. The aim of this study was to evaluate the intraspecific variability of morphological characters that are most often used inAcantholaimustaxonomy, in order to distinguish those which are most informative for species differentiation. A reverse taxonomic approach was applied for initial species discrimination. Two loci, one each from small and large subunits of rRNA, were sequenced for 59Acantholaimusspecimens from two deep-sea locations. Twenty-seven Molecular Operational Taxonomic Units (MOTU) were identified, of which 12 were represented by more than one individual. These were then analysed for intraspecific variability in morphological characters. Some of the examined characters showed high intraspecific variability; specifically: length of cephalic setae; distance from anterior end to amphid; shape of anterior setae; position and arrangement of cervical setae. In the absence of genetic data, these characters should be used with caution for differential diagnoses or species discrimination. Other characters were more conservative within the same MOTU: body proportions; length of outer labial setae; amphidial diam.; appearance of lateral field; general arrangement of cervical setae; and shape of tail. These characters may be successfully used for species discrimination in the absence of molecular data.

Morphological and genetic variability of Baetis (Rhodobaetis) braaschi Zimmermann, 1980 (Ephemeroptera: Baetidae)

Zootaxa ◽  
2012 ◽  
Vol 3323 (1) ◽  
pp. 27 ◽  
Author(s):  
PAVEL SROKA ◽  
ALEXANDER V. MARTYNOV ◽  
ROMAN J. GODUNKO
Keyword(s):  
Genetic Variability ◽  
Methodological Approach ◽  
Morphological Variability ◽  
Geographic Origin ◽  
Intraspecific Variability ◽  
Morphological Data ◽  
Mtdna Coi ◽  
Geographic Regions ◽  
Coi Sequences ◽  
The Individual

Specimens of Baetis (Rhodobaetis) braaschi Zimmermann, 1980 from the three distant geographic regions (Crimean Pen-insula, Eastern Ukraine and Caucasus) are investigated and compared using a methodological approach combining mor-phological and molecular (partial mtDNA COI sequences) data. Intraspecific variability in several morphologicalcharacters is recognized and described, whereas COI sequences are found to be very uniform. The amount and distributionof the changes of COI sequences do not follow the pattern of morphological variability and/or geographic origin of thespecimens. This indicates that analysis of the changes in the COI sequence can contradict the pattern of morphologicalcharacters commonly used for the discrimination of the individual Rhodobaetis species. As a basis for the future taxonom-ic changes concerning subgenus Rhodobaetis, it is advised (where possible) to critically evaluate both molecular and morphological data.

scholarly journals Genetic characterization of Genista sericea Wulfen (Cytiseae – Fabaceae) as revealed by nuclear DNA content and its nrDNA region analysis

2012 ◽  
Vol 71 (2) ◽  
pp. 195-205
Author(s):  
Liliana Vižintin ◽  
Vera Kosovel ◽  
Laura Feoli Chiapella
Keyword(s):  
Dna Content ◽  
Nuclear Dna ◽  
Morphological Variability ◽  
Geographic Origin ◽  
Nuclear Dna Content ◽  
Intraspecific Variability ◽  
Its Region ◽  
Its Nrdna ◽  
Morphological Differences ◽  
Northern Croatia

Summary-Genista sericeaWulfen, a northern Illyrian amphi-Adriatic species, presents a certain morphological variability. To clarify whether the genetic variations support the morphological differences among accessions of different geographic origin, analysis of nuclear DNA content and polymorphism of the internal transcribed spacer (ITS) dataset was studied. The variation in nuclear DNA content ofG. sericeavar.sericeaand var.rigidais minimal (2.09 and 2.08 pg/nucleus respectively) and is correlated with equal chromosome numbers in both varieties. Intraspecific variability of the ITS region was studied on 13 accessions ofG. sericea, 6 belonging to var.sericeaand 7 to var.rigida. These accessions were analyzed in comparison to closely related species already studied. ITS sequences ofG. sericearevealed large polymorphism and formed two main clusters. One cluster (6 accessions) comprehends var.sericeaof northern Italy, Slovenia and northern Croatia; the other cluster (7 accessions) includes five accessions of var.rigidafrom southern Croatia and Montenegro and two from the Pollino massif (southern Italy). The later two accessions considerably differed from other accessions of var.rigida. This genetic analysis supports the previous assumptions, which subdividedG. sericeainto at least two taxa. On the basis of the results presented, it is here suggested that the subdivision ofG. sericeainto var.sericeaand var.rigidashould be maintained.

scholarly journals Genetic diversity of pomegranate germplasm collection from Spain determined by fruit, seed, leaf and flower characteristics

2016 ◽  
Author(s):  
Juan José Martínez ◽  
Pablo Melgarejo ◽  
Pilar Legua ◽  
Francisco García ◽  
Francisca Hernández
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Plant Material ◽  
Phenotypic Variability ◽  
Geographical Area ◽  
Geographic Origin ◽  
Germplasm Management ◽  
Morphometric Characteristics ◽  
Germplasm Bank ◽  
Improvement Programs

Background . Miguel Hernandez University ( Spain ) created a germplasm bank of the varieties of pomegranate from different Southeastern Spain localities in order to preserve the crop’s wide genetic diversity. Once this collection was established, the next step was to characterize the phenotype of these varieties to determine the phenotypic variability that existed among all the different pomegranate genotypes, and to understand the degree of polymorphism of the morphometric characteristics among varieties. Methods. Fifty-three pomegranate (Punica granatum L.) accessions were studied in order to determine their degree of polymorphism and to detect similarities in their genotypes. Thirty-one morphometric characteristics were measured in fruits, arils, seeds, leaves and flowers, as well as juice characteristics including content, pH, titratable acidity, total soluble solids and maturity index. ANOVA, principal component analysis, and cluster analysis showed that there was a considerable phenotypic diversity (and presumably genetic). Results. The cluster analysis produced a dendrogram with four main clusters. The dissimilarity level ranged from 1 to 25, indicating that there were varieties that were either very similar or very different from each other, with varieties from the same geographical areas being more closely related. Within each varietal group, different degrees of similarity were found, although there were no accessions that were identical. These results highlight the crop’s great genetic diversity, which can be explained not only by their different geographical origins, but also to the fact that these are native plants that have not come from genetic improvement programs. The geographic origin could be, in the cases where no exchanges of plant material took place, a key criterion for cultivar clustering. Conclusions. As a result of the present study, we can conclude that among all the parameters analyzed, those related to fruit and seed size as well as the juice’s acidity and pH had the highest power of discrimination, and were, therefore, the most useful for genetic characterization of this pomegranate germplasm banks. This is opposed to leaf and flower characteristics, which had a low power of discrimination. This germplasm bank, more specifically, was characterized by its considerable phenotypic (and presumably genetic) diversity among pomegranate accessions, with a greater proximity existing among the varieties from the same geographical area, suggesting that over time, there had not been an exchange of plant material among the different cultivation areas. In summary, knowledge on the extent of the genetic diversity of the collection is essential for germplasm management. In this study, these data may help in developing strategies for pomegranate germplasm management and may allow for more efficient use of this germplasm in future breeding programs for this species.

scholarly journals The Molecular Epidemiology of Cystic and Alveolar Echinococcosis in Southeast Turkey

2021 ◽  
Author(s):  
Fadime Eroglu ◽  
Mehmet Dokur ◽  
Yüksel Ulu
Keyword(s):  
Infectious Diseases ◽  
Molecular Epidemiology ◽  
Real Time ◽  
Real Time Pcr ◽  
Environmental Changes ◽  
Phylogenetic Analyses ◽  
Geographical Area ◽  
Epidemiological Studies ◽  
Genotype 3 ◽  
Southeast Region

Background: The migration of humans and climatic and environmental changes cause the emergence of infectious diseases. This study aimed to investigate the changes in the molecular epidemiology of the echinococcosis in the southeast region of Turkey after migrations. Methods: Overall, 159 tissues samples were taken from suspected cases of echinococcosis at the Kilis State Hospital in the southeast region of Turkey. All of the tissues samples were analyzed using histopathology methods, PCR, Real-time PCR methods, DNA sequencing, and phylogenetic analyses in laboratories. Results: The positivity values of the histopathology, the polymerase chain reaction, and the Real-time PCR methods were found to be 14.5% (23/159), 15.7% (25/159), and 16.9% (27/159), respectively. 32.0 % (8/25) E. multilocularis of Echinococcus isolates and 68% (17/25) E. granulosus of Echinococcus isolates were identified using PCR methods. 58.8% (10/17) of the E. granulosus isolates were found to be Genotype 1% and 41.2% (7/17) E. granulosus isolates were found to be Genotype 3. Conclusion: Molecular methods play an important role in the epidemiology, treatment, and diagnosis of diseases. Increasing immigration in a geographical area may create social, economic, and health problems in that area. For this reason, epidemiological studies of infectious diseases should be updated in areas with immigration.

Expanded RAS and BRAF V600 testing as predictive biomarkers for single agent cetuximab in the randomized phase III CO.17 trial.

2019 ◽  
Vol 37 (4_suppl) ◽  
pp. 537-537 ◽  
Author(s):  
Jonathan M. Loree ◽  
Anthony Dowers ◽  
Dongsheng Tu ◽  
Christopher J. O'Callaghan ◽  
Dan Edelstein ◽  
...  
Keyword(s):  
Single Agent ◽  
Predictive Biomarkers ◽  
Digital Pcr ◽  
Phase Iii ◽  
Molecular Profile ◽  
Braf Mutations ◽  
Exon 2 ◽  
Archival Tissue ◽  
Frequency Detection ◽  
Kras Exon

537 Background: KRAS/NRAS ( RAS) testing of exons 2, 3 and 4 is standard prior to anti-EGFR treatment in metastatic colorectal cancer and many consider BRAFV600 ( BRAF) mutations predictive. CO.17 was a randomized phase III trial comparing cetuximab vs best supportive care (BSC) in unselected patients (pts). Re-analysis tested only KRAS exon 2, thus the benefit of cetuximab in RAS/BRAF wild type (WT) pts is unclear. Methods: We retrospectively performed expanded RAS/BRAF testing using a highly sensitive digital PCR method (BEAMing; 1% allele frequency detection limit) on micro-dissected archival tissue from 248 CO.17 pts. Additional pts without available archival tissue, with prior Sanger sequencing or therascreen results were included in analyses if mutations were previously detected (n = 77). Overall survival (OS), progression free survival (PFS), and response rates (RR) were compared by molecular profile. Results: Of 248 sequenced pts, 139 (56%) were RAS mutant, with 112 (45%) exon 2, 11 (4%) exon 3 and 6 (2%) exon 4 KRAS mutant, and 10 (4%) NRAS mutant pts. Seven (3%) BRAF mutant, and 97 (30%) confirmed RAS/BRAF WT pts were identified. Results are summarized below. A test of interaction indicated RAS status was predictive for PFS (p = 0.0001) and OS (p = 0.037) and BRAF status neared significance as a predictive marker for PFS (p = 0.089) but not OS (p = 0.24). Conclusions: These updated results demonstrate an improved PFS (HR 0.25 vs 0.40 previously) and OS (HR 0.51 vs 0.55 previously) for cetuximab in RAS/BRAF WT pts compared to prior analyses that included only KRAS exon 2 mutation status. We provide an estimate of single agent cetuximab efficacy for future anti-EGFR re-challenge studies and demonstrate further support that BRAF mutations may predict lack of benefit from anti-EGFR therapy. Clinical trial information: NCT00079066. [Table: see text]

scholarly journals Evaluating Precipitation Estimates from Eta, TRMM and CHRIPS Data in the South-Southeast Region of Minas Gerais State—Brazil

2018 ◽  
Vol 10 (3) ◽  
pp. 313 ◽  
Author(s):  
Sulimar Caparoci Nogueira ◽  
Maurício Moreira ◽  
Margarete Lordelo Volpato
Keyword(s):  
Minas Gerais ◽  
The South ◽  
Southeast Region ◽  
Minas Gerais State ◽  
Precipitation Estimates

scholarly journals Phylogenetic Analysis and Molecular Typing of Trichothecene-Producing Fusarium Fungi from Russian Collections

Acta Naturae ◽  
2018 ◽  
Vol 10 (2) ◽  
pp. 79-92
Author(s):  
A. A. Stakheev ◽  
L. V. Samokhvalova ◽  
O. D. Mikityuk ◽  
S. K. Zavriev
Keyword(s):  
Phylogenetic Analysis ◽  
Fusarium Species ◽  
Geographic Origin ◽  
Elongation Factor ◽  
Intraspecific Variability ◽  
North Caucasus ◽  
The North ◽  
Group I ◽  
High Level ◽  
First Time

We performed a three-locus phylogenetic analysis of Fusarium strains presumably capable of trichothecene production, which were deposited in the Russian national collections. The intra- and interspecific polymorphism of partial sequences of the translation elongation factor 1 alpha (TEF1) gene and two genes from the trichothecene cluster TRI5 and TRI14 was studied. A study of 60 strains of different origins using DNA markers confirmed, and in the case for several strains, clarified their taxonomic characteristics. As a result, a strain of F. commune (F-900) was identified in Russia for the first time. Furthermore, the strain F-846 proved to be phylogenetically distinct from any of the known Fusarium species. F. equiseti strains from Northwest Russia were found to belong to the North European group (I), whereas a strain from the North Caucasus - to the South European one (II). Partial TRI14 sequences from 9 out of 12 species were determined for the first time. Their comparative analysis demonstrated a relatively high level of intraspecific variability in F. graminearum and F. sporotrichioides, but no correlation between the sequence polymorphism and the geographic origin of the strains or their chemotype was found. Specific chemotypes of trichothecene B producers were characterized using two primer sets. The chemotyping results were verified by HPLC.

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