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.

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 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.

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.

Morphological variation in Nereis (Neanthes) virens (Polychaeta: Nereididae) populations

2004 ◽  
Vol 84 (5) ◽  
pp. 983-985 ◽  
Author(s):  
Sophie Breton ◽  
France Dufresne ◽  
Gaston Desrosiers ◽  
Pierre Blier
Keyword(s):  
Cluster Analysis ◽  
Gene Flow ◽  
Phenotypic Plasticity ◽  
Morphological Variation ◽  
Genetic Study ◽  
Group Method ◽  
Restricted Gene Flow ◽  
Pair Group ◽  
Morphological Variants ◽  
Unweighted Pair Group Method

The intraspecific variation in the number and distribution of paragnaths in ten populations of Nereis (Neanthes) virens collected throughout its range was examined. Significant differences among populations are found in the total number of paragnaths and in each paragnath group. The unweighted pair-group method using arithmetic averages cluster analysis revealed three distinct clusters separating Canadian populations, Europe/USA populations and the Japanese population, suggesting the implication of either restricted gene flow, selection on paragnath patterns or phenotypic plasticity. Comparison with a previous genetic study suggests that morphological variants represent ecotypes of the single, widely distributed N. virens species.

RAPD analysis of cultivated and wild yellow nutsedge (Cyperus esculentusL.)

Weed Science ◽  
1998 ◽  
Vol 46 (3) ◽  
pp. 318-321 ◽  
Author(s):  
Paloma Abad ◽  
Bernardo Pascual ◽  
José V. Maroto ◽  
Salvador López-Galarza ◽  
María J. Vicente ◽  
...  
Keyword(s):  
Rapd Markers ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Group Method ◽  
Wild Populations ◽  
Arithmetic Average ◽  
Yellow Nutsedge ◽  
Pair Group ◽  
High Level ◽  
Unweighted Pair Group Method

Cultivated and weedy clones of yellow nutsedge were analyzed using random amplified polymorphic DNA (RAPD) markers to assess the polymorphism within the species and determine if this approach was suitable for identification of cultivar and wild populations. The RAPD markers unambiguously identified all studied clones. Nei-Li similarities were computed and used in an unweighted pair group method using arithmetic average (UPGMA) cluster analyses. Cultivated and weedy clones were clustered in two groups, but two cultivated clones were more closely related to weedy clones than to cultivated clones. The results showed a high level of genetic variability among the clones tested, particularly among the cultivated ones. Identification of yellow nutsedge cultivars and analysis of genetic diversity within and among weedy populations is possible by using only a small number of primers. In this study, seven selected primers discriminated among the 10 tested clones.

scholarly journals Diversidade genética entre acessos de maracujazeiros com base em descritores morfoagronômicos

2021 ◽  
Vol 8 (1) ◽  
pp. 4-10
Author(s):  
Thalita Neves Marostega ◽  
Severino de Paiva Sobrinho ◽  
Petterson Baptista da Luz
Keyword(s):  
Group Method ◽  
Passiflora Edulis ◽  
Mato Grosso ◽  
Pair Group ◽  
Passiflora Foetida ◽  
Unweighted Pair Group Method

Este trabalho teve como finalidade estimar a diversidade genética entre acessos de maracujazeiros conservados na coleção de trabalho da Universidade do Estado de Mato Grosso, com base em descritores morfoagronômicos. O experimento foi conduzido em delineamento de blocos ao acaso, com quatro repetições, quatro plantas por parcela. Foi gerada uma matriz de dissimilaridade fundamentada no complemento do coeficiente de coincidência simples. De acordo com os valores da matriz de dissimilaridade, os acessos Passiflora morifolia e Passiflora foetida foram os mais similares (dii’ 0,25), enquanto os acessos Passiflora quadrangularis e Passiflora suberosa foram os mais distantes (dii’ 0,88). Os acessos mais divergentes com base no método unweighted pair-group method with arithmetic averages (UPGMA) foram P. foetida e Passiflora edulis, sendo ambos pertencentes a subgêneros distintos.

scholarly journals METODE TRANSFORMASI CAKAR AYAM UNTUK MEREDUKSI SEARCH-SPACE PADA INTRUSION DETECTION SYSTEM BERBASIS K-NEAREST NEIGHBOR

2016 ◽  
Vol 2 (2) ◽  
Author(s):  
Kharisma Muchammad ◽  
Thomas Brian
Keyword(s):  
Intrusion Detection ◽  
Intrusion Detection System ◽  
Nearest Neighbor ◽  
Detection System ◽  
Search Space ◽  
Group Method ◽  
K Nearest Neighbor ◽  
Pair Group ◽  
Space Reduction ◽  
Unweighted Pair Group Method

[Id] Penggunaan Intrusion Detection System (IDS) pada jaringan komputer merupakan hal yang diperlukan untuk menjaga keamanan jaringan. Beberapa IDS berbasis K-nearest neighbor (KNN) memiliki akurasi yang relatif baik namun jika data training terlalu besar, waktu yang diperlukan untuk mendeteksi serangan juga meningkat. Waktu untuk deteksi bisa ditekan dengan mereduksi search space pada data training. Namun problem reduksi search space dengan mempertahankan kualitas deteksi masih merupakan problem terbuka. Pada artikel ini diajukan suatu metode transformasi "cakar ayam" berbasis jumlah jarak data ke centroid dan jarak data ke dua sub-centroid untuk mereduksi search space pada IDS berbasis K-nearest neighbor. Localized K-nearest neighbor dilakukan pada data yang telah tertransformasi. Eksperimen menggunakan agglome-rative hierarchial clustering dengan Unweighted Pair-Group Method of Centroid pada dataset NSL-KDD 20% menunjukkan penurunan search space maksimum sebesar 38% dengan tingkat akurasi sebesar 77.5%. Tingkat akurasi dan specificity maksimum yang dicapai pada eksperimen sebesar 88% dan 88.3% dengan tingkat reduksi sebesar 12% dan tingkat sensitifity maksimum yang dicapai sebesar 80.2% pada tingkat reduksi 11%. Berdasarkan eksperimen, luas search space dapat dikurangi sambil menjaga akurasi deteksi. Rasio tradeoff antara akurasi dan search space mungkin dapat diperbaiki dengan mengganti algortima clustering dengan divisive hierarchial clustring. Abstract : clustering, deteksi intrusi, keamanan jaringan [En] Intrusion detection System (IDS) for computer network has became an essential needs to ensure network security. Some K-nearest neighbor (KNN) based IDS have a relatively good accracy in detecting attack, but the need to use all training data costs time consumption . Detection time cost can be reduced by reducing search space needed for the algorithm. The problem of search space reduction while maintaining decent accuracy still an open problem. In this Paper we propose a new transformation method "chiken claw" method. which based on sum of two distances. The first distance is the distance of data and its cluster. The later is distance of data to 2 of its cluster's sub-centroid..This method is proposed to reduce the search space on K-nearest neighbor based IDS because the search is based on resulted one dimentional transformed data. Experiment using Unweighted Pair-group Method of centroid on NSL-KDD 20% shows maximum search space reduction 38% with 75% accuracy. Maximum accuracy and sensitivity in the experiment is 88% and 88.3% respectively with space reduction 12%. Maximum sensitivity from experiment is at 80.2% with 11% space reduction. Based on experiments, search space can be reduced while maintaining accuracy. Search space-accuracy trade off might be improved by using different clustering algorithm such as divisive hierarchial clustering

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