Genomic relatedness ofStaphylococcus aureusphages of the International Typing Set and detection of serogroup A, B, and F prophages in lysogenic strains

2000 ◽  
Vol 46 (11) ◽  
pp. 1066-1076 ◽  
Author(s):  
Jiri Doškar ◽  
Petra Pallová ◽  
Roman Pantucek ◽  
Stanislav Rosypal ◽  
Vladislava Ruzicková ◽  
...  
Keyword(s):  
Genomic Dna ◽  
The Other ◽  
Restriction Map ◽  
Restriction Maps ◽  
Separate Species ◽  
Restriction Patterns ◽  
Genomic Dnas ◽  
Time Restriction ◽  
Genomic Relatedness ◽  
Restriction Enzyme Maps

On the basis of HindIII-restriction digest analysis of genomic DNAs, the S. aureus bacteriophages of the International Typing Set were divided into five clusters designated as A, F, Ba, Bb, and Bc. The clusters A and F include all the phages of serogroups A and F and correspond to species 3A and 77 proposed by Ackermann and DuBow (1987). On the other hand, the phages of serogroup B were divided into three clusters designated as Ba, Bb, and Bc that differ significantly each from the other in their restriction patterns. The clusters Ba and Bb may represent two separate species, while the cluster Bc may include more than one phage species. For each of the phage serogroups A, B, and F, common HindIII-restriction fragments of phage 3A (1700 bp), of 53 (4060 bp), and of 77 (8300 bp) were used for the preparation of probes specific to the phages of serogroups A, B, and F. These probes were very effective, making it possible to detect up to three different prophages in a given lysogenic strain at the same time. Restriction enzyme maps of phages 3A, 53, and 77, each representing a different serogroup, were constructed. The restriction maps of phage 3A and that of phage 77 are linear, whereas that of phage 53 is circular and exhibits a circular permutation. DNAs of the phages of serogroups A and F have cohesive ends. On each restriction map, the sites corresponding to specific probes are indicated. The size of intact genomic DNA of all phages estimated by PFGE varies within the range of 41.5-46.2 kb.Key words: Staphylococcus aureus, bacteriophages, prophage specific probes, restriction endonuclease maps.

scholarly journals Comparative Analysis of Geolocation Information through Mobile-Devices under Different COVID-19 Mobility Restriction Patterns in Spain

2021 ◽  
Vol 10 (2) ◽  
pp. 73
Author(s):  
Raquel Pérez-Arnal ◽  
David Conesa ◽  
Sergio Alvarez-Napagao ◽  
Toyotaro Suzumura ◽  
Martí Català ◽  
...  
Keyword(s):  
Mobile Phones ◽  
Human Mobility ◽  
The Other ◽  
Data Sources ◽  
Experimental Setting ◽  
Mobile Data ◽  
Restriction Patterns ◽  
Mobility Data ◽  
The World ◽  
Proper Interpretation

The COVID-19 pandemic is changing the world in unprecedented and unpredictable ways. Human mobility, being the greatest facilitator for the spread of the virus, is at the epicenter of this change. In order to study mobility under COVID-19, to evaluate the efficiency of mobility restriction policies, and to facilitate a better response to future crisis, we need to understand all possible mobility data sources at our disposal. Our work studies private mobility sources, gathered from mobile-phones and released by large technological companies. These data are of special interest because, unlike most public sources, it is focused on individuals rather than on transportation means. Furthermore, the sample of society they cover is large and representative. On the other hand, these data are not directly accessible for anonymity reasons. Thus, properly interpreting its patterns demands caution. Aware of that, we explore the behavior and inter-relations of private sources of mobility data in the context of Spain. This country represents a good experimental setting due to both its large and fast pandemic peak and its implementation of a sustained, generalized lockdown. Our work illustrates how a direct and naive comparison between sources can be misleading, as certain days (e.g., Sundays) exhibit a directly adverse behavior. After understanding their particularities, we find them to be partially correlated and, what is more important, complementary under a proper interpretation. Finally, we confirm that mobile-data can be used to evaluate the efficiency of implemented policies, detect changes in mobility trends, and provide insights into what new normality means in Spain.

scholarly journals Extraction of genomic DNA from Melipona quadrifasciata (Hymenoptera: Apidae, Meliponinae)

1997 ◽  
Vol 20 (3) ◽  
pp. 421-423 ◽  
Author(s):  
Ana Maria Waldschmidt ◽  
Tânia Maria Fernandes Salomão ◽  
Everaldo Gonçalves de Barros ◽  
Lúcio de Antônio Oliveira Campos
Keyword(s):  
Dna Extraction ◽  
Genomic Dna ◽  
Stingless Bee ◽  
The Other ◽  
Melipona Quadrifasciata ◽  
Other Hand ◽  
Extraction Buffer

The objective of the present study was to test three different procedures for DNA extraction of Melipona quadrifasciata based on existing methods for DNA extraction of Apis, plants and fungi. These methods differ in the concentrations of specific substances in the extraction buffer. The results demonstrate that the method used for Apis is not adequate for DNA extraction from M. quadrifasciata. On the other hand, with minor modifications this method and the methods for plants and fungi were adequate for DNA extraction of this stingless bee, both for adults and larvae

scholarly journals Taxonomy of Micronesian monitors (Reptilia: Squamata: Varanus ): endemic status of new species argues for caution in pursuing eradication plans

2020 ◽  
Vol 7 (5) ◽  
pp. 200092
Author(s):  
Valter Weijola ◽  
Varpu Vahtera ◽  
André Koch ◽  
Andreas Schmitz ◽  
Fred Kraus
Keyword(s):  
New Species ◽  
The Other ◽  
Disjunct Distribution ◽  
Morphological Evidence ◽  
Mariana Islands ◽  
Separate Species ◽  
Natural Origin ◽  
Phylogenetic Studies ◽  
Human Introduction ◽  
Monitor Lizards

In the light of recent phylogenetic studies, we re-assess the taxonomy and biogeography of the Varanus populations distributed in the Micronesian islands of Palau, the Western Carolines and the Marianas. Whether these populations are of natural origin or human introductions has long been contentious, but no study has fully resolved that question. Here, we present molecular and morphological evidence that monitor lizards of the Varanus indicus Group reached both Palau and the Mariana Islands sometime in the late Pleistocene and subsequently differentiated into two separate species endemic to each geographical region. One species is confined to the Mariana Islands, and for these populations, we revalidate the name V. tsukamotoi Kishida, 1929. The other species has a disjunct distribution in Palau, the Western Carolines and Sarigan Island in the Northern Marianas and is herein described as V. bennetti sp. nov. Both species are most closely allied to each other, V. lirungensis and V. rainerguentheri , suggesting that colonization of Micronesia took place from the Moluccas. We discuss the biogeographic distributions of both species in the light of the likely colonization mechanism and previous arguments for human introduction, and we argue that bounties for Palauan populations are ill-advised and plans for eradication of some other populations must first demonstrate that they are, in fact, introduced and not native.

scholarly journals Genetic diversity and structure of the binturong Arctictis binturong (Carnivora: Viverridae) – status of the elusive Palawan binturong and implications for conservation

2019 ◽  
Author(s):  
Géraldine Veron ◽  
Agathe Debruille ◽  
Pauline Kayser ◽  
Desamarie Antonette P Fernandez ◽  
Aude Bourgeois
Keyword(s):  
Taxonomic Status ◽  
The Philippines ◽  
The Other ◽  
Restricted Range ◽  
Crucial Importance ◽  
Separate Species ◽  
Mitochondrial Markers ◽  
Molecular Approaches ◽  
Captive Populations ◽  
Genetic Diversity And Structure

Abstract The binturong or bearcat is a forest mesocarnivore ranging from Nepal to Indonesia and the Philippines. Several subspecies of binturongs are recognized but a revision is needed. The binturong from Palawan was described as a species and is now considered a subspecies, but its status has never been checked using molecular approaches. Owing to its restricted range and the pressure on its habitat, the Palawan binturong may be endangered. It is, therefore, of crucial importance to clarify its taxonomic status, particularly for the management of captive populations. We sequenced one nuclear and two mitochondrial markers for binturongs from locations across the species range and from zoos. Our results provide an assessment of the genetic polymorphism and structure within the binturong, resulting in two groups, corresponding to the Indochinese and the Sundaic regions. Within the latter were found the Palawan binturongs on one side, and an individual from Sulu archipelago (a locality not reported before) on the other side. The Palawan binturongs form a monophyletic group, genetically close to Bornean binturongs, which suggests that they may have dispersed from Borneo, and represents a lineage worth preserving, but which is not a separate species nor a separate subspecies.

Trachelomonas volzii vs T. dubia (Euglenophyceae)—one or two separate species? Study on similarities and differences of the species

Phytotaxa ◽  
2018 ◽  
Vol 357 (1) ◽  
pp. 1 ◽  
Author(s):  
MAŁGORZATA PONIEWOZIK ◽  
KONRAD WOŁOWSKI ◽  
JOLANTA PIĄTEK
Keyword(s):  
Electron Microscopy ◽  
The Other ◽  
New Combinations ◽  
Separate Species ◽  
Phenotypic Changes ◽  
The World ◽  
Key Features ◽  
Similarities And Differences ◽  
Species Study ◽  
Scanning Electron

This study concerns the two species Trachelomonas volzii and T. dubia which were examined for similarities and dissimilarities of their loricae and monads organization. We specifically focused on the key features of both species that were originally used to separate one from the other: annular thickening at the base of collar and dimensions and ornamentation of loricae. Loricae of specimens were examined by light and scanning electron microscopy and the results were compared with the literature data describing these taxa and reported occurrences in the world. The species together with their varieties and forms do not appear to have strong characteristics distinguishing them, rather the variability observed fits natural phenotypic changes. Based on evidence from this study, we recommend combining these two taxa and propose T. volzii as the single taxon. We also examined a set of varieties of original T. volzii since the species contained several varieties that were almost identical in relation to lorica structure and occurrence. As a result of these observations, we propose the following varieties: Trachelomonas volzii var. volzii as a nominative variety, T. volzii var. australis, T. volzii var. sulcata, T. volzii var. inflata, T. volzii var. acidophila. Furthermore, we propose reclassifying some taxa and the new combinations such as: T. dubia var. ornata to T. volzii var. ornata and T. dubia var. colliundulata to T. volzii var. colliundulata. In our opinion, T. dubia fo. acuminata should be included with the species T. hexangulata due to its unique, hexagonal shaped lorica.

Functional aspects of cytidine-guanosine dinucleotides and their locations in genes

2011 ◽  
Vol 2 (5) ◽  
pp. 391-405 ◽  
Author(s):  
Franz Varga ◽  
Heidrun Karlic ◽  
Roman Thaler ◽  
Klaus Klaushofer
Keyword(s):  
Gene Expression ◽  
Genomic Instability ◽  
Genome Organization ◽  
Genomic Dna ◽  
Methylation Status ◽  
Cpg Islands ◽  
The Other ◽  
Functional Aspects ◽  
Development And Differentiation ◽  
Organizational Features

AbstractOriginally, the finding of a particular distribution of cytidine-guanosine dinucleotides (CpGs) in genomic DNA was considered to be an interesting structural feature of eukaryotic genome organization. Despite a global depletion of CpGs, genes are frequently associated with CpG clusters called CpG islands (CGIs). CGIs are prevalently unmethylated but often found methylated in pathologic situations. On the other hand, CpGs outside of CGIs are generally methylated and are found mainly in the heterochromatic fraction of the genome. Hypomethylation of those CpGs is associated with genomic instability in malignancy. Additionally, CpG-rich and CpG-poor regions, as well as CpG-shores, are defined. Usually, the methylation status inversely correlates with gene expression. Methylation of CpGs, as well as demethylation and generation of hydroxmethyl-cytosines, is strictly regulated during development and differentiation. This review deals with the relevance of the organizational features of CpGs and their relation to each other.

Restriction enzyme and DNA hybridization analysis of cellulolytic Streptomyces isolates of different origin

1997 ◽  
Vol 43 (4) ◽  
pp. 395-399 ◽  
Author(s):  
Laura Marri ◽  
Emanuela Barboni ◽  
Tiziana Irdani ◽  
Brunella Perito ◽  
Giorgio Mastromei
Keyword(s):  
Restriction Enzyme ◽  
Dna Hybridization ◽  
Genomic Dna ◽  
Restriction Pattern ◽  
Enzyme Analysis ◽  
Restriction Enzyme Analysis ◽  
Restriction Maps ◽  
E Coli ◽  
The One ◽  
Different Sources

Streptomyces rochei A2 endoglucanase (eglS) and β-glucosidase (bgs1) genes were used as probes to survey their distribution among 16 Streptomyces strains isolated from different sources and characterized for their cellulolytic activities. The eglS probe hybridized to the genomic DNA of 12 strains with a restriction pattern different from that of S. rochei A2. The DNA from all strains, except one, hybridized with the bgsl probe and one strain showed the same restriction pattern as seen in S. rochei A2. The sequence localized by the eglS probe in S. thermoviolaceus and the one localized by the bgs1 probe in strain EC1 were cloned and expressed in E. coli in plasmids pTAE and pCSF203, respectively. The restriction maps showed that the cloned genes were identical to eglS and bgs1. The restriction enzyme analysis of genomic DNA from all the strains identified nine different groups, each characterized by a distinctive pattern and in agreement with the results of the hybridization experiments.Key words: Streptomyces, cellulase genes, hybridization, restriction enzyme analysis.

Cytological studies of subterranean clover (Trifolium subterraneum L.)

1952 ◽  
Vol 3 (3) ◽  
pp. 300 ◽  
Author(s):  
JJ Yates ◽  
NH Brittan
Keyword(s):  
Chromosome Number ◽  
Somatic Chromosome ◽  
Subterranean Clover ◽  
Trifolium Subterraneum ◽  
The Other ◽  
Vicia Sativa ◽  
Somatic Chromosome Number ◽  
Separate Species ◽  
Apparent Relationship ◽  
Isolated Species

Somatic chromosome number and morphology in certain strains of subterranean clover and in species of several other fairly closely related genera have been observed. Dwalganup, Yarloop, Mt. Barker, Wenigup, Burnerang, and Red Leaf strains have each 16 fairly small chromosomes, the chromosome complexes being similar to one another and to that obtained by Wexelsen (1928) for the species. Palestine and Israel strains have each 12 large chromosomes, bearing no apparent relationship to those of the other strains but being the same in number and of a similar order of size to those found in Vicia sativa. Chromosome number and morphology may explain the failure to obtain intervarietal crosses involving Palestine, but not the low percentage of successful crosses between other strains. It is suggested that perhaps Palestine and Israel may be more correctly classed as strains of a separate species and that, with regard to their origin, Wexelsen's idea of mutational changes in isolated species offers probably the best explanation.

scholarly journals Anti-liver kidney microsome antibody recognizes a cytochrome P450 from the IID subfamily.

1988 ◽  
Vol 168 (2) ◽  
pp. 801-806 ◽  
Author(s):  
M Gueguen ◽  
M Meunier-Rotival ◽  
O Bernard ◽  
F Alvarez
Keyword(s):  
Cytochrome P450 ◽  
Rat Liver ◽  
Fusion Proteins ◽  
Expression Vector ◽  
High Serum ◽  
Nucleotide Sequencing ◽  
Restriction Map ◽  
Restriction Maps ◽  
Liver Cdna Library ◽  
Kidney Microsome

Children with autoimmune hepatitis have high serum titers of antibodies directed against a 50-kD protein of rat liver endoplasmic reticulum. Affinity-purified anti-50-kD antibodies were used to screen a rat liver cDNA library in lambda GT-11 expression vector. 12 immunopositive clones were obtained. Crossreactivities between fusion proteins of these clones and the 50-kD protein was demonstrated, and four clones were analyzed by restriction mapping, one of them by nucleotide sequencing. Complete identity was found between the restriction maps of two clones (LKMC1 and LKMC2) and that of the 5' end of the rat cytochrome P450 db2. Sequence of a 608-bp fragment of LKMC1 showed complete homology with the rat P450 db2 form. The restriction map of the other two clones (LKMC3 and LKMC4) was identical to that of rat P450 db1. These results suggest that the antigen recognized by LKMA is a P450 of the IID subfamily.

scholarly journals Molecular relaxation processes in genomic DNA from leaf tissues: A surface-enhanced Raman spectroscopic study

2011 ◽  
Vol 26 (4-5) ◽  
pp. 245-254 ◽  
Author(s):  
Cristina M. Muntean ◽  
Ioan Bratu ◽  
Nicolae Leopold
Keyword(s):  
Genomic Dna ◽  
Metallic Surface ◽  
Relaxation Processes ◽  
Molecular Subgroups ◽  
Molecular Relaxation ◽  
Data Set ◽  
Surface Enhanced ◽  
Surface Enhanced Raman ◽  
Leaf Tissues ◽  
Genomic Dnas

In this work the SERS total half bandwidths of six genomic DNAs from ex vitro-grown apple leaf tissues (Malus domesticaBorkh., Fam. Rosaceae, cvs. Rebra, Goldrush, Florina, Romus 4, and the rootstocks M26, M9) and of five genomic DNAs fromin vitrogrown plants ofArnica montana(L.), Fam. Compositae,Astragalus peterfii(Jáv.), Fam. Fabaceae, strawberry (Duch.), Fam. Rosaceae, carnation (Dianthus caryophyllusL.), Fam. Caryophyllaceae, andKalanchoe x hybrida, Fam. Crassulaceae, respectively, have been measured. We have shown that surface-enhanced Raman scattering can be used to study the fast subpicosecond dynamics of DNA in the proximity of a metallic surface. The dependencies of the total half bandwidths and of the global relaxation times, on DNA molecular subgroup structure and on the type of genomic DNA, are reported.It is shown that changes in the subpicosecond surface dynamics of molecular subgroups in genomic DNAs from leaf tissues can be monitored with surface-enhanced Raman spectroscopy. In our study, the full widths at half-maximum (FWHMs) for the SERS bands of genomic DNAs from different leaf tissues, are typically in the wavenumber range from 15 to 30 cm–1for data set 1 and from 13 to 42 cm–1for data set 2. Besides, it can be observed that molecular relaxation processes studied in this work, have a global relaxation time smaller than 0.71 ps and larger than 0.35 ps (data set 1) and also varying between 0.25–0.82 ps for data set 2. A comparison between different ranges of FT-Raman and SERS band parameters, respectively, of DNA extracted from leaf tissues is given. We have found that the bands of DNA from Florina cultivar and Kalanchoe leaves, respectively, are suitable for the study of dynamical behaviour of molecular subgroups in nucleic acids extracted from different leaf tissues.

Sign in / Sign up

Export Citation Format

Share Document