scholarly journals Putative Transposases Conserved in Exiguobacterium Isolates from Ancient Siberian Permafrost and from Contemporary Surface Habitats

2005 ◽  
Vol 71 (11) ◽  
pp. 6954-6962 ◽  
Author(s):  
Tatiana A. Vishnivetskaya ◽  
Sophia Kathariou
Keyword(s):  
Surface Water ◽  
High Resolution ◽  
Food Processing ◽  
Microbial Mats ◽  
Genomic Diversity ◽  
Insertion Sequences ◽  
Gram Positive Bacteria ◽  
Lake Fryxell ◽  
Siberian Permafrost ◽  
Type Strains

ABSTRACT Gram-positive bacteria of the genus Exiguobacterium have been repeatedly isolated from Siberian permafrost ranging in age from 20,000 to 2 to 3 million years and have been sporadically recovered from markedly diverse habitats, including microbial mats in Lake Fryxell (Antarctic), surface water, and food-processing environments. However, there is currently no information on genomic diversity of this microorganism or on the physiological strategies that have allowed its survival under prolonged freezing in the permafrost. Analysis of the genome sequence of the most ancient available Exiguobacterium isolate (Exiguobacterium sp. strain 255-15, from 2 to 3 million-year-old Siberian permafrost) revealed numerous putative transposase sequences, primarily of the IS200/IS605, IS30, and IS3 families, with four transposase families identified. Several of the transposase genes appeared to be part of insertion sequences. Southern blots with different transposase probes yielded high-resolution genomic fingerprints which differentiated the different permafrost isolates from each other and from the Exiguobacterium spp. type strains which have been derived from diverse surface habitats. Each of the Exiguobacterium sp. strain 255-15 transposases that were used as probes had highly conserved homologs in the genome of other Exiguobacterium strains, both from permafrost and from modern sites. These findings suggest that, prior to their entrapment in permafrost, Exiguobacterium isolates had acquired transposases and that conserved transposases are present in Exiguobacterium spp., which now can be isolated from various modern surface habitats.

scholarly journals Genomic diversity of Mycobacterium avium subsp. paratuberculosis: pangenomic approach for highlighting unique genomic features with newly constructed complete genomes

2021 ◽  
Vol 52 (1) ◽  
Author(s):  
Jaewon Lim ◽  
Hong-Tae Park ◽  
Seyoung Ko ◽  
Hyun-Eui Park ◽  
Gyumin Lee ◽  
...  
Keyword(s):  
Mycobacterium Avium ◽  
Phenotypic Diversity ◽  
Control Strategies ◽  
Genomic Diversity ◽  
Phenotypic Traits ◽  
Whole Genome ◽  
Genomic Features ◽  
Phenotypic Differences ◽  
Mycobacterium Avium Subsp Paratuberculosis ◽  
Type Strains

AbstractMycobacterium avium subsp. paratuberculosis (MAP) is a causative agent of Johne’s disease, which is a chronic granulomatous enteropathy in ruminants. Determining the genetic diversity of MAP is necessary to understand the epidemiology and biology of MAP, as well as establishing disease control strategies. In the present study, whole genome-based alignment and comparative analysis were performed using 40 publicly available MAP genomes, including newly sequenced Korean isolates. First, whole genome-based alignment was employed to identify new genomic structures in MAP genomes. Second, the genomic diversity of the MAP population was described by pangenome analysis. A phylogenetic tree based on the core genome and pangenome showed that the MAP was differentiated into two major types (C- and S-type), which was in keeping with the findings of previous studies. However, B-type strains were discriminated from C-type strains. Finally, functional analysis of the pangenome was performed using three virulence factor databases (i.e., PATRIC, VFDB, and Victors) to predict the phenotypic diversity of MAP in terms of pathogenicity. Based on the results of the pangenome analysis, we developed a real-time PCR technique to distinguish among S-, B- and C-type strains. In conclusion, the results of our study suggest that the phenotypic differences between MAP strains can be explained by their genetic polymorphisms. These results may help to elucidate the diversity of MAP, extending from genomic features to phenotypic traits.

scholarly journals Tracking late Pleistocene Neandertals on the Iberian coast

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Eduardo Mayoral ◽  
Ignacio Díaz-Martínez ◽  
Jéremy Duveau ◽  
Ana Santos ◽  
Antonio Rodríguez Ramírez ◽  
...  
Keyword(s):  
High Resolution ◽  
Iberian Peninsula ◽  
Social Group ◽  
Microbial Mats ◽  
3D Models ◽  
Age Classes ◽  
Upper Pleistocene ◽  
Wide Range ◽  
The World ◽  
Flooded Area

AbstractHere, we report the recent discovery of 87 Neandertal footprints on the Southwest of the Iberian Peninsula (Doñana shoreline, Spain) located on an upper Pleistocene aeolian littoral setting (about 106 ± 19 kyr). Morphometric comparisons, high resolution digital photogrammetric 3D models and detailed sedimentary analysis have been provided to characterized the footprints and the palaeoenvironment. The footprints were impressed in the shoreline of a hypersaline swamped area related to benthic microbial mats, close to the coastline. They have a rounded heel, a longitudinal arch, relatively short toes, and adducted hallux, and represent the oldest upper Pleistocene record of Neandertal footprints in the world. Among these 87 footprints, 31 are longitudinally complete and measure from 14 to 29 cm. The calculated statures range from 104 to 188 cm, with half of the data between 130 and 150 cm. The wide range of sizes of the footprints suggests the existence of a social group integrated by individuals of different age classes but dominated, however, by non-adult individuals. The footprints, which are outside the flooded area are oriented perpendicular to the shoreline. These 87 footprints reinforce the ecological scenario of Neandertal groups established in coastal areas.

scholarly journals Two-Step Urban Water Index (TSUWI): A New Technique for High-Resolution Mapping of Urban Surface Water

2018 ◽  
Vol 10 (11) ◽  
pp. 1704 ◽  
Author(s):  
Wei Wu ◽  
Qiangzi Li ◽  
Yuan Zhang ◽  
Xin Du ◽  
Hongyan Wang
Keyword(s):  
Surface Water ◽  
High Resolution ◽  
Urban Surface ◽  
Mapping Technique ◽  
Support Vector ◽  
Svm Classifier ◽  
P Value ◽  
Urban Water ◽  
Water Index ◽  
Water Mapping

Urban surface water mapping is essential for studying its role in urban ecosystems and local microclimates. However, fast and accurate extraction of urban water remains a great challenge due to the limitations of conventional water indexes and the presence of shadows. Therefore, we proposed a new urban water mapping technique named the Two-Step Urban Water Index (TSUWI), which combines an Urban Water Index (UWI) and an Urban Shadow Index (USI). These two subindexes were established based on spectral analysis and linear Support Vector Machine (SVM) training of pure pixels from eight training sites across China. The performance of the TSUWI was compared with that of the Normalized Difference Water Index (NDWI), High Resolution Water Index (HRWI) and SVM classifier at twelve test sites. The results showed that this method consistently achieved good performance with a mean Kappa Coefficient (KC) of 0.97 and a mean total error (TE) of 2.28%. Overall, classification accuracy of TSUWI was significantly higher than that of the NDWI, HRWI, and SVM (p-value < 0.01). At most test sites, TSUWI improved accuracy by decreasing the TEs by more than 45% compared to NDWI and HRWI, and by more than 15% compared to SVM. In addition, both UWI and USI were shown to have more stable optimal thresholds that are close to 0 and maintain better performance near their optimum thresholds. Therefore, TSUWI can be used as a simple yet robust method for urban water mapping with high accuracy.

scholarly journals High Resolution Melting Analysis for Rapid Mutation Screening in Gyrase and Topoisomerase IV Genes in Quinolone-ResistantSalmonella enterica

2014 ◽  
Vol 2014 ◽  
pp. 1-8 ◽  
Author(s):  
Soo Tein Ngoi ◽  
Kwai Lin Thong
Keyword(s):  
High Resolution ◽  
Mutation Screening ◽  
Rapid Screening ◽  
Health Concern ◽  
Wild Type ◽  
High Resolution Melt ◽  
Topoisomerase Iv ◽  
Melting Analysis ◽  
Type Strains ◽  
Difference Plot

The increasedSalmonellaresistance to quinolones and fluoroquinolones is a public health concern in the Southeast Asian region. The objective of this study is to develop a high resolution melt curve (HRM) assay to rapidly screen for mutations in quinolone-resistant determining region (QRDR) of gyrase and topoisomerase IV genes. DNA sequencing was performed on 62Salmonellastrains to identify mutations in the QRDR ofgyrA,gyrB,parC, andparEgenes. Mutations were detected in QRDR ofgyrA(n=52; S83F, S83Y, S83I, D87G, D87Y, and D87N) andparE(n=1; M438I).Salmonellastrains with mutations within QRDR ofgyrAare generally more resistant to nalidixic acid (MIC16>256 μg/mL). Mutations were uncommon within the QRDR ofgyrB,parC, andparEgenes. In the HRM assay, mutants can be distinguished from the wild-type strains based on the transition of melt curves, which is more prominent when the profiles are displayed in difference plot. In conclusion, HRM analysis allows for rapid screening for mutations at the QRDRs of gyrase and topoisomerase IV genes inSalmonella. This assay markedly reduced the sequencing effort involved in mutational studies of quinolone-resistance genes.

High-resolution mass spectrometry-based selection of peanut peptide biomarkers considering food processing and market type variation

2020 ◽  
Vol 304 ◽  
pp. 125428 ◽  
Author(s):  
Maxime Gavage ◽  
Kaatje Van Vlierberghe ◽  
Christof Van Poucke ◽  
Marc De Loose ◽  
Kris Gevaert ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
High Resolution ◽  
Food Processing ◽  
High Resolution Mass Spectrometry ◽  
High Resolution Mass ◽  
Selection Of ◽  
Resolution Mass

scholarly journals Environmental controls on bacteriohopanepolyol profiles of benthic microbial mats from Lake Fryxell, Antarctica

Geobiology ◽  
2019 ◽  
Vol 17 (5) ◽  
pp. 551-563 ◽  
Author(s):  
Emily D. Matys ◽  
Tyler Mackey ◽  
Christen Grettenberger ◽  
Elliott Mueller ◽  
Anne Jungblut ◽  
...  
Keyword(s):  
Microbial Mats ◽  
Environmental Controls ◽  
Lake Fryxell

The Surface Water Acidification Project (SWAP) Palaeolimnology Programme

1990 ◽  
Vol 327 (1240) ◽  
pp. 227-232 ◽  
Keyword(s):  
Surface Water ◽  
High Resolution ◽  
Lake Sediment ◽  
Water Acidification ◽  
Diatom Analysis ◽  
Atmospheric Contamination ◽  
Surface Water Acidification ◽  
History Of ◽  
Study Sites ◽  
Water Acidity

Improvements in techniques of lake-sediment analysis over the last two decades have enabled palaeolimnologists to reconstruct changes in water acidity and atmospheric contamination with high resolution. In the Surface Water Acidification Project (SWAP) Palaeolimnology Programme these techniques have been used to trace the history of a range of specially selected study sites and to evaluate alternative causes for lake acidification. At the same time further improvements in some of the techniques, especially diatom analysis, have been made.

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