scholarly journals Molecular Diversity and Genetic Relatedness of Candida albicans Isolates from Birds in Hungary

2021 ◽  
Vol 186 (2) ◽  
pp. 237-244
Author(s):  
M. Domán ◽  
L. Makrai ◽  
Gy. Lengyel ◽  
R. Kovács ◽  
L. Majoros ◽  
...  
Keyword(s):  
Candida Albicans ◽  
Molecular Diversity ◽  
Genetic Relatedness ◽  
Group Method ◽  
Pair Group ◽  
Degree Of Separation ◽  
Avian Origin ◽  
Species Specific ◽  
Sequence Types ◽  
Unweighted Pair Group Method

AbstractThe molecular epidemiology of Candida albicans infections in animals has been rarely studied. In this study, multilocus sequence typing was used to characterise the genetic diversity and population structure of 24 avian origin C. albicans isolates collected from different birds with candidiasis and compared to human isolates. Fourteen diploid sequence types (DSTs) including six new DSTs were determined. Cluster analysis revealed that isolates grouped into 8 clades. Bird isolates mainly belonged to minor clades and Clade 15 with DST 172 was the most common (11 isolates; 45.8%). The remaining isolates were clustered into Clade 7 (5 isolates; 20.8%), Clade 10 (4 isolates; 16.6%), Clade 8 (2 isolates; 8.3%), Clade 4 (1 isolate; 4.2%) and Clade 16 (1 isolate; 4.2%). Unweighted pair group method with arithmetic averages (UPGMA) and eBURST analyses showed that the genetic construction of avian origin C. albicans population is fairly diverse. Although species-specific lineages were not found, some degree of separation in the evolution of bird and human strains could be observed.

scholarly journals Padrões de infestação de comunidades de plantas daninhas no agroecossistema de cana-crua

2008 ◽  
Vol 26 (3) ◽  
pp. 549-557 ◽  
Author(s):  
M.A. Kuva ◽  
A.S. Ferraudo ◽  
R.A. Pitelli ◽  
P.L.C.A. Alves ◽  
T.P. Salgado
Keyword(s):  
Group Method ◽  
Pair Group ◽  
Unweighted Pair Group Method

Objetivou-se neste trabalho a obtenção de padrões de infestação de plantas daninhas na cultura de cana-de-açúcar com histórico de colheita mecanizada sem queima prévia da palha. Foram realizadas amostragens em 28 talhões na região de Ribeirão Preto, SP; em cada talhão foram demarcadas unidades de avaliação e coleta, na proporção de duas por hectare, que consistiram de áreas (quatro linhas de 4 metros de comprimento) mantidas sem controle de plantas daninhas e onde foram realizadas as amostragens de plantas emergidas. As amostragens foram realizadas aos 120 dias após o corte, com quadrados vazados (0,5 x 0,5 m) lançados aleatoriamente duas vezes em cada uma das unidades de avaliação e coleta. Com os dados obtidos, calculou-se a importância relativa e o índice de agregação das espécies ou grupo de espécies. Esses índices foram usados no processamento da análise de agrupamento hierárquica, utilizando como medida de semelhança a distância euclidiana e como estratégia de agrupamento o método UPGMA (Unweighted Pair-Group Method using arithmetic Averages). Foi possível distinguir quatro grupos em função da importância relativa e cinco grupos de talhões em função do índice de agregação; dentro de alguns grupos houve formação de subgrupos.

scholarly journals Caracterização Biométrica dos Caprinos da República de Cabo Verde

2019 ◽  
Vol 68 (263) ◽  
pp. 384-394
Author(s):  
L.C. Pires ◽  
T.M. Machado ◽  
J. de D. Fonseca ◽  
J.F. Fonseca ◽  
E. Pile ◽  
...  
Keyword(s):  
Arithmetic Mean ◽  
Group Method ◽  
Cabo Verde ◽  
Pair Group ◽  
Unweighted Pair Group Method

Objetivou-se discernir populações caprinas de cinco ilhas da República de Cabo Verde (n=533) por meio de dados biométricos e análises estatísticas. Foram avaliadas 16 características de fêmeas adultas, através da estatística descritiva simples, análise de variância, teste de multicolinearidade, distância generalizada de Mahalanobis (D²) e algoritmo UPGMA (Unweighted Pair Group Method Arithmetic Mean). Após o teste de multicolinearidade foi identificada e descartada a variável profundidade torácica. As D² foram calculadas com base nas 15 medidas biométricas. O maior valor da D² foi entre as populações das ilhas do Fogo e São Nicolau (22,73), e a menor D² foi entre Santo Antão e São Vicente (3,71). O dendrograma a partir de 15 variáveis em cinco populações colocou as cabras da ilha de Fogo em ramo a parte das demais. Agruparam-se num ramo as cabras das ilhas de Santo Antão e São Vicente. Este resultado está de acordo com a distância geográfica entre as ilhas de Cabo Verde e o histórico recente de intercâmbio de animais entre elas.

scholarly journals Hospital Specificity, Region Specificity, and Fluconazole Resistance of Candida albicans Bloodstream Isolates

1998 ◽  
Vol 36 (6) ◽  
pp. 1518-1529 ◽  
Author(s):  
M. A. Pfaller ◽  
S. R. Lockhart ◽  
C. Pujol ◽  
J. A. Swails-Wenger ◽  
S. A. Messer ◽  
...  
Keyword(s):  
United States ◽  
Drug Resistance ◽  
Candida Albicans ◽  
Genetic Relatedness ◽  
Computer Assisted ◽  
Specific Probe ◽  
Fluconazole Resistance ◽  
Fluconazole Resistant ◽  
Species Specific ◽  
Close Genetic Relationship

In a survey of bloodstream infection (BSI) isolates across the continental United States, 162 Candida albicans isolates were fingerprinted with the species-specific probe Ca3 and the patterns were analyzed for relatedness with a computer-assisted system. The results demonstrate that particular BSI strains are more highly concentrated in particular geographic locales and that established BSI strains are endemic in some, but not all, hospitals in the study and undergo microevolution in hospital settings. The results, however, indicate no close genetic relationship among fluconazole-resistant BSI isolates in the collection, either from the same geographic locale or the same hospital. This study represents the first of three fingerprinting studies designed to analyze the origin, genetic relatedness, and drug resistance of Candida isolates responsible for BSI.

scholarly journals Identificação de parentais e híbridos entre Vitis vinifera e Vitis rotundifolia utilizando polimorfismo enzimático e marcador RAPD

Bragantia ◽  
1996 ◽  
Vol 55 (2) ◽  
pp. 221-230 ◽  
Author(s):  
Haiko Enok Sawazaki ◽  
Celso Valdevino Pommer ◽  
Ilene Ribeiro Da Silva Passos ◽  
Maurilo Monteiro Terra ◽  
Erasmo José Paioli Pires
Keyword(s):  
Vitis Vinifera ◽  
Random Amplified Polymorphic Dna ◽  
Group Method ◽  
Vitis Rotundifolia ◽  
Pair Group ◽  
Unweighted Pair Group Method

Identificaram-se parentais e híbridos entre Vitis vinifera (videiras comuns) e V. rotundifolia (muscadínias), utilizando-se o polimorfismo enzimático e marcador RAPD (Random Amplified Polymorphic DNA). Os sistemas GOT (glutamato-oxalo-acetato-transaminase), IDH (isocitrato desidrogenase) e PGI (fosfoglucose isomerase) diferenciaram a muscadínia, sendo observadas cinco aloenzimas para o GOT, duas para o LAP (leucina aminopeptidase) e quatro para o EST (esterase). Os sistemas PGI e IDH apresentaram-se como diméricos com o fenótipo de quatro aloenzimas em duas regiões e três em uma região respectivamente. O marcador RAPD apresentou polimorfismo que permitiu a diferenciação entre todos os cultivares. Os dendrogramas UPGMA (unweighted pair-group method with aritmetic mean) obtidos pelas isoenzimas e pelo marcador RAPD foram semelhantes, sendo a aproximação mais forte entre 'Itália' e 'Rubi' que se ligaram aos cultivares Patrícia e A Dona. Os cultivares Piratininga e Eugênio, também bastante próximos, foram os seguintes a se ligarem às demais viníferas. Pelo polimorfismo enzimático e marcador RAPD, a muscadínia ficou bastante isolada dos outros grupos. Pelo método RAPD, aplicado às muscadínias, ao híbrido da Carolina do Norte NC66 C203-9, a um possível híbrido e seu parental feminino, observou-se o seguinte: os híbridos foram intermediários às muscadínias e viníferas, porém o possível híbrido se assemelhou ao parental feminino, enquanto o NC66203-9 apresentou bandas provenientes das muscadínias e viníferas, comprovando sua origem híbrida.

scholarly journals Filogenetik Human papillomavirus (HPV) tipe 6 dan tipe 11 pada penderita recurrent respiratory papillomatosis

2014 ◽  
Vol 44 (1) ◽  
pp. 52
Author(s):  
Lenny Buana Wuriningtyas ◽  
Dwi Reno Pawarti ◽  
Achmad Chusnu Romdhoni
Keyword(s):  
Phylogenetic Tree ◽  
Dna Sequences ◽  
Arithmetic Mean ◽  
Recurrent Respiratory Papillomatosis ◽  
Open Reading Frame ◽  
Group Method ◽  
Cross Sectional ◽  
Reading Frame ◽  
Pair Group ◽  
Unweighted Pair Group Method

Latar belakang: Papiloma saluran pernapasan berulang (recurrent respiratory papillomatosis/RRP) merupakan neoplasma jinak laring terbanyak akibat infeksi HPV tipe 6 dan tipe 11. RRP merupakan masalah terkait agresivitas dan terapi. Analisis genetik digunakan untuk membedakan varian HPV tipe 6 dan tipe 11. Filogenetik mengevaluasi evolusi sequen DNA virus. Tujuan: Penelitian bertujuan mengidentifikasi sequen DNA dan menganalisis pohon filogenetik HPV tipe 6 dan tipe 11 pada papiloma saluran pernapasan berulang. Metode: Penelitian merupakan observasional deskriptif cross sectional. Analisis menggunakan data pembanding dari GenBank. Filogenetik disusun menggunakan metodeUPGMA (Unweighted Pair Group Method with Arithmetic Mean). Didapatkan 15 sampel jaringan papiloma. Dilakukan pemeriksaan PCR dan analisis sequen DNA. Hasil: Dari 15 sampel penelitian (12 laki-laki, 3 perempuan) didapatkan 9 isolat HPV tipe 6 (8 varian dan 1 subtipe) dan 4 isolat HPV tipe 11 (3 varian dan 1 subtipe). Terdapat mutasi titik yang mengakibatkan munculnya varian dan subtipe HPV tipe 6 maupun tipe 11. Kesimpulan: sequen DNA sampel berasal dari L1 ORF (Late 1 Open Reading Frame) yang merupakan kapsid mayor virus. Proses mutasi level gen berupa substitusi, insersi, dan delesi.Subtipe HPV tipe 6 dan tipe 11 yang ditemukan diperkirakan sebagai subtipe baru dan belum pernah dilaporkan sebelumnya. Lima varian HPV tipe 6 membentuk satu cabang tersendiri pada nomenklatur filogenetik yang sudah ada sehingga diajukan sebagai sublineage baru (sublineage C). Seluruh isolat HPV tipe 11 membentuk cabang pohon tersendiri dan diajukan sebagai sublineage baru (sublineage B).Kata kunci: HPV tipe 6 dan 11, variasi sequen DNA, pohon filogenetik HPV tipe 6 and 11. ABSTRACTBackground: Recurrent respiratory papillomatosis (RRP) is the most common laryngeal benign neoplasm caused by infection of HPV type 6 and 11. RRP is still a serious problem related to agresivity and therapy. Genetic analysis used to determine the variant of HPV type 6 or 11. Phylogenetic tree used to evaluate the evolution of viral DNA squence. Purpose: This study aimed to identify DNA squences and analyse the phylogenetic tree of HPV type 6 and 11 in RRP. Methods: this was a descriptive observational cross sectional study. Data analysis used GenBank database and phylogenetic tree was constructed usedUPGMA (Unweighted Pair Group Method with Arithmetic Mean). 15 papillomas biopsies from RRP patients subjected HPV typing using PCR dan DNA sequensing analysis. Result: From 15 patients with RRP (12 male, 3 female), there were 9 isolates HPV type 6 (8 variants, 1 subtype) and 4 isolates HPV type 11 (3 variants, 1 subtype). There was a point mutation in HPV type 6 and 11. Conclusion: L1 ORF (Late 1 Open Reading Frame) sequensials DNA samples was virus major capsid. There were mutational process at gene level (substitution, insertion, deletion). Subtype of HPV-6 and 11, might be new ones, and had not been reported yet. Five variants of HPV type 6 constructed a different lineage in phylogenetic and it is proposed to be C sublineage. All samples HPV type 11 proposed as B sublineage. Keywords: HPV type 6 and 11, DNA sequences variations, phylogenetic trees HPV type 6 and 11.

scholarly journals MOLECULAR CHARACTERIZATION OF QUALITY PROTEIN MAIZE AND DOWNY MILDEW RESISTANCE LINES BASED ON SIMPLE SEQUENCE REPEATS (SSRs) MARKER

Zuriat ◽  
2015 ◽  
Vol 16 (1) ◽  
Author(s):  
D. Ruswandi ◽  
N. Wicaksana ◽  
M. B. Pabendon ◽  
M. Azrai ◽  
M. Rachmadi ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Genetic Relationship ◽  
Genetic Relatedness ◽  
Genotypic Variation ◽  
Group Method ◽  
Maize Breeding ◽  
Pair Group ◽  
Group A ◽  
Ssrs Markers ◽  
Relationship Of

The information on germplasm diversity and genetic relatedness among elite breeding materials is an important element in maize breeding. Molecular characterization and genetic relationship of 11 QPM-DMR lines were analysed using thirty three SSRs markers. Genetic relationship was determined using Jaccard’s similarity coefficient, and dendogram was then constructed based on the unweighted pair-group method with arithmetical averages (UPGMA). Result showed that (i) all SSRs loci were informative for describing the genotypic variation as showed by their PIC, which ranged from 0.19 for umc1304 to 0.93 for phi112; (ii) the eleven maize inbred lines were clustered into one major group A and small groups B and C that corresponds well with the breeding programs adopted at different institutes of release, and (iii) thus, SSRs marker system is a valuable marker for varietals identification and for genetic diversity study of elite breeding materials.

scholarly journals Differentiation of Lactobacillus species by ARDRA

2013 ◽  
Vol 31 (No. 2) ◽  
pp. 180-188 ◽  
Author(s):  
K. Kšicová ◽  
M. Dušková ◽  
R. Karpíšková
Keyword(s):  
Restriction Analysis ◽  
Rapid Identification ◽  
Starter Cultures ◽  
Lactobacillus Species ◽  
Group Method ◽  
Jaccard Coefficient ◽  
Pair Group ◽  
Genus Lactobacillus ◽  
Dna Restriction ◽  
Species Specific

The Lactobacillus species by 16S Amplified Ribosomal DNA Restriction Analysis (16S-ARDRA) was identified. Lactobacilli are bacteria often found in foodstuffs of both animal and vegetable origins. On one hand, they play an important role in the food spoilage and, on the other hand, they are used as starter cultures in food fermentation processes. The species-specific identification by traditional biochemical methods is time consuming and not always fully effective. Therefore, more efficient techniques are searched for. We focused on rapid identification of Lactobacillus isolates from different habitats. Forty-nine collection strains and isolates belonging to the genus Lactobacillus were discriminated. ARDRA was carried out with two restriction endonucleases. For the comparison of similarity, the Jaccard coefficient and clustering by the unweighted pair group method with arithmetic averages (UPGMA) were used. The percentages of similarity between profiles varied from 22% to 100% (AluI) and from 27% to 100% (MspI). This method proved applicable to the differentiation of 10 species.  

Macrogeographic Genetic Variation in Populations of the Webbing Cone worm (Lepidoptera: Pyralidae)

1995 ◽  
Vol 30 (3) ◽  
pp. 349-358 ◽  
Author(s):  
James A. Richmond
Keyword(s):  
North Carolina ◽  
Genetic Variation ◽  
Genetic Structure ◽  
Genetic Identity ◽  
Group Method ◽  
Cophenetic Correlation ◽  
Pair Group ◽  
Starch Gel ◽  
Lepidoptera Pyralidae ◽  
Unweighted Pair Group Method

Genetic variation among 14 populations of Dioryctria disclusa Heinrich adults was examined using starch gel electophoresis. The average number of alleles per locus exceeded 2.0 in all populations. The number of polymorphic loci exceeded 70% in 11 populations. Genetic structure data suggest moderate differentiation (average Fst, 0.111) among the populations. Most of the differentiation is attributable to three of the eight loci (MDH, ME, and IDH). Nei's genetic identity ranged from 0.77–1.00 between populations. A phenogram based on genetic identity and unweighted pair-group method of analysis (UPGMA) clustered five of six populations in North Carolina closely together. With a cophenetic correlation of 0.96 the phenogram constructed is acceptable.

Halotolerant Bacillus diversity in hypersaline environments

1998 ◽  
Vol 44 (2) ◽  
pp. 95-102 ◽  
Author(s):  
M J Garabito ◽  
M C Márquez ◽  
A Ventosa
Keyword(s):  
Group Method ◽  
Identification System ◽  
Saline Soils ◽  
Hypersaline Environments ◽  
Numerical Techniques ◽  
Genus Bacillus ◽  
Halotolerant Bacteria ◽  
Microbial Identification ◽  
Pair Group ◽  
Unweighted Pair Group Method

A total of 99 Gram-positive aerobic endospore-forming halotolerant rods were isolated from different hypersaline sources in Spain (salterns as well as saline soils). They were characterized taxonomically for a total of 178 features, including the utilization of 95 different substrates determined by the Biolog microbial identification system. These results were analysed by numerical techniques using the Jaccard (SJ) coefficient and clustering was achieved using the unweighted pair group method with averages algorithm. At 60% similarity level, the majority of the isolates were clustered in seven phenons. The guanine plus cytosine (G + C) content of some representative strains selected from each phenon ranged from 36.0 to 50.4 mol%. The isolates were identified as members of the genus Bacillus, and were assigned to the species B. pantothenticus, B. firmus, B. alcalophilus, B. megaterium, and B. laterosporus. They were extremely halotolerant, most were able to grow in media with up to 20 or 25% salt. The diversity of groups and characteristics of the halotolerant Bacillus isolated in this study indicate that they may play an important ecological role and contribute to the microbial diversity of hypersaline environments.Key words: halotolerant bacteria, Bacillus, taxonomy, hypersaline environments.

Genetic relatedness among cultivated and wild mulberry (Moraceae: Morus) as revealed by inter-simple sequence repeat analysis in China

2006 ◽  
Vol 86 (1) ◽  
pp. 251-257 ◽  
Author(s):  
Zhao Weiguo ◽  
Zhou Zhihua ◽  
Miao Xuexia ◽  
Wang Sibao ◽  
Zhang Lin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Genetic Relatedness ◽  
Genetic Relationships ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Group Method ◽  
Sequence Repeat ◽  
Pair Group ◽  
Simple Sequence

The genetic diversity of 27 mulberry (Morus spp.) genotypes mainly from China was investigated using inter-simple sequence repeat (ISSR) markers to assist in addressing breeding objectives and conserving existing genetic resources. Of the 22 primers screened, 15 produced highly reproducible ISSR bands. Using these 15 primers, 138 discernible DNA fragments were generated with 126 (91.3%) being polymorphic, indicating considerable genetic variation among the mulberry genotypes studied. Genetic similarity ranged from 0.6014 between Yu 2 and Yu 711 to 0.9493 between Cuizhisang and Dejiang 10. The phenetic dendrogram based on ISSR data generated by the unweighed pair group method with arithmetical averages (UPGMA) method grouped the 27 accessions into two major clusters: cluster I, cultivated mulberry species (M. multicaulis Perr., M. alba Linn., M. atropurpurea oxb., M. bombycis Kiodz., M. australis Poir., M. rotundiloba Kiodz., M. alba var. pendula Dipp., M. alba var. macrophylla Loud., and M. alba var. venose Delile.); and cluster II, wild mulberry species (M. cathayana Hemsl., M. laevigata Wall., M. wittiorum Hand-Mazz., M. nigra Linn., and M. mongolica Schneid.). Our molecular analyses agree with the existing morphological classification of Morus and clarify the genetic relationships among mulberry species. Key words: Morus L., genetic diversity, inter-simple sequence repeat, relatedness

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