scholarly journals Wide-Range Distribution of Insertion Sequences Identified in B. halodurans among Bacilli and a New Transposon Disseminated in Alkaliphilic and Thermophilic Bacilli

DNA Research ◽  
2004 ◽  
Vol 11 (3) ◽  
pp. 153-162 ◽  
Author(s):  
H. Takami
Keyword(s):  
Insertion Sequences ◽  
Range Distribution ◽  
Thermophilic Bacilli ◽  
Wide Range

scholarly journals ISMapper: Identifying insertion sequences in bacterial genomes from short read sequence data

2015 ◽  
Author(s):  
Jane Hawkey ◽  
Mohammad Hamidian ◽  
Ryan R Wick ◽  
David J Edwards ◽  
Helen Billman-Jacobe ◽  
...  
Keyword(s):  
Sequence Data ◽  
Insertion Sequences ◽  
Bacterial Genomes ◽  
Short Read ◽  
Phenotypic Resistance ◽  
Genome Wide ◽  
Wide Range ◽  
Multiple Copies ◽  
Short Read Sequence ◽  
Insertion Sites

Background Insertion sequences (IS) are small transposable elements, commonly found in bacterial genomes. Identifying the location of IS in bacterial genomes can be useful for a variety of purposes including epidemiological tracking and predicting antibiotic resistance. However IS are commonly present in multiple copies in a single genome, which complicates genome assembly and the identification of IS insertion sites. Here we present ISMapper, a mapping-based tool for identification of the site and orientation of IS insertions in bacterial genomes, direct from paired-end short read data. Results ISMapper was validated using three types of short read data: (i) simulated reads from a variety of species, (ii) Illumina reads from 5 isolates for which finished genome sequences were available for comparison, and (iii) Illumina reads from 7 Acinetobacter baumannii isolates for which predicted IS locations were tested using PCR. A total of 20 genomes, including 13 species and 32 distinct IS, were used for validation. ISMapper correctly identified 96% of known IS insertions in the analysis of simulated reads, and 98% in real Illumina reads. Subsampling of real Illumina reads to lower depths indicated ISMapper was reliable for average genome-wide read depths >20x. All ISAba1 insertions identified by ISMapper in the A. baumannii genomes were confirmed by PCR. In each A. baumannii genome, ISMapper successfully identified an IS insertion upstream of the ampC beta-lactamase that could explain phenotypic resistance to third-generation cephalosporins. The utility of ISMapper was further demonstrated by profiling genome-wide IS6110 insertions in 138 publicly available Mycobacterium tuberculosis genomes, revealing lineage-specific insertions and multiple insertion hotspots. Conclusions ISMapper provides a rapid and robust method for identifying IS insertion sites direct from short read data, with a high degree of accuracy demonstrated across a wide range of bacteria.

scholarly journals Isolation and Characterization of Thermophilic Bacilli Degrading Cinnamic, 4-Coumaric, and Ferulic Acids

2003 ◽  
Vol 69 (3) ◽  
pp. 1417-1427 ◽  
Author(s):  
Xue Peng ◽  
Norihiko Misawa ◽  
Shigeaki Harayama
Keyword(s):  
Vanillic Acid ◽  
Hot Spring ◽  
Aromatic Acids ◽  
Gentisic Acid ◽  
Isolation And Characterization ◽  
Thermophilic Bacilli ◽  
Wide Range ◽  
Thermophilic Conditions ◽  
Hydroxybenzoic Acids ◽  
Hydroxypropionic Acid

ABSTRACT Thirty-four thermophilic Bacillus sp. strains were isolated from decayed wood bark and a hot spring water sample based on their ability to degrade vanillic acid under thermophilic conditions. It was found that these bacteria were able to degrade a wide range of aromatic acids such as cinnamic, 4-coumaric, 3-phenylpropionic, 3-(p-hydroxyphenyl)propionic, ferulic, benzoic, and 4-hydroxybenzoic acids. The metabolic pathways for the degradation of these aromatic acids at 60°C were examined by using one of the isolates, strain B1. Benzoic and 4-hydroxybenzoic acids were detected as breakdown products from cinnamic and 4-coumaric acids, respectively. The β-oxidative mechanism was proposed to be responsible for these conversions. The degradation of benzoic and 4-hydroxybenzoic acids was determined to proceed through catechol and gentisic acid, respectively, for their ring fission. It is likely that a non-β-oxidative mechanism is the case in the ferulic acid catabolism, which involved 4-hydroxy-3-methoxyphenyl-β-hydroxypropionic acid, vanillin, and vanillic acid as the intermediates. Other strains examined, which are V0, D1, E1, G2, ZI3, and H4, were found to have the same pathways as those of strain B1, except that strains V0, D1, and H4 had the ability to transform 3-hydroxybenzoic acid to gentisic acid, which strain B1 could not do.

scholarly journals Molecular and Genomic Characterization of PFAB2: A Non-virulent Bacillus anthracis Strain Isolated from an Indian Hot Spring

2020 ◽  
Vol 20 (7) ◽  
pp. 491-507 ◽  
Author(s):  
Aparna Banerjee ◽  
Vikas K. Somani ◽  
Priyanka Chakraborty ◽  
Rakesh Bhatnagar ◽  
Rajeev K. Varshney ◽  
...  
Keyword(s):  
Bacillus Anthracis ◽  
Culture Media ◽  
Draft Genome ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Taxonomic Resolution ◽  
Thermophilic Bacilli ◽  
Wide Range ◽  
Genomic Characterization

Background: Thermophilic bacilli in both aerobic or facultative anaerobic forms have been isolated for over a hundred years from different mesophilic or thermophilic environments as they are potential source of bioactive secondary metabolites. But the taxonomic resolution in the Bacillus genus at species or at strain level is very challenging for the insufficient divergence of the 16S rRNA genes. One such recurring problem is among Bacillus anthracis, B. cereus and B. thuringiensis. The disease-causing B. anthracis strains have their characteristic virulence factors coded in two wellknown plasmids, namely pXO1 (toxin genes) and pXO2 (capsule genes). Objective: The present study aimed at the molecular and genomic characterization of a recently reported thermophilic and environmental isolate of B. anthracis, strain PFAB2. Methods: We performed comparative genomics between the PFAB2 genome and different strains of B. anthracis, along with closely related B. cereus strains. Results: The pangenomic analysis suggests that the PFAB2 genome harbors no complete prophage genes. Cluster analysis of Bray-Kurtis similarity resemblance matrix revealed that gene content of PFAB2 is more closely related to other environmental strains of B. anthracis. The secretome analysis and the in vitro and in vivo pathogenesis experiments corroborate the avirulent phenotype of this strain. The most probable explanation for this phenotype is the apparent absence of plasmids harboring genes for capsule biosynthesis and toxins secretion in the draft genome. Additional features of PFAB2 are good spore-forming and germinating capabilities and rapid replication ability. Conclusion: The high replication rate in a wide range of temperatures and culture media, the nonpathogenicity, the good spore forming capability and its genomic similarity to the Ames strain together make PFAB2 an interesting model strain for the study of the pathogenic evolution of B. anthracis.

scholarly journals Anoxybacillus ayderensis sp. nov. and Anoxybacillus kestanbolensis sp. nov.

2004 ◽  
Vol 54 (5) ◽  
pp. 1499-1503 ◽  
Author(s):  
Sabriye Dulger ◽  
Zihni Demirbag ◽  
Ali Osman Belduz
Keyword(s):  
Dna Hybridization ◽  
Hot Springs ◽  
Carbon Sources ◽  
Rrna Gene ◽  
Moderately Thermophilic ◽  
Hybridization Data ◽  
Thermophilic Bacilli ◽  
Wide Range ◽  
Anoxybacillus Flavithermus ◽  
Type Strains

Two thermophilic bacilli were isolated from mud and water samples of the Ayder and Kestanbol hot springs in the provinces of Rize and Canakkale, respectively, in Turkey. Strains AB04T and K4T were sporulating, Gram-positive, rod-shaped bacteria. These isolates were moderately thermophilic (with an optimum temperature for growth of 50–55 °C), facultative anaerobes able to grow on a wide range of carbon sources including d-glucose, d-raffinose, d-sucrose, d-xylose, d-fructose, l-arabinose, maltose, d-mannose and d-mannitol. Analysis of the 16S rRNA gene sequences showed that these isolates resembled Anoxybacillus flavithermus DSM 2641T and Anoxybacillus gonensis NCIMB 13933T. DNA–DNA hybridization data revealed that thermophilic isolate AB04T has only 51·2 % relatedness to A. flavithermus, 45·1 % relatedness to Anoxybacillus pushchinoensis and 68·6 % relatedness to A. gonensis. Thermophilic isolate K4T showed only 60·4 % relatedness to A. flavithermus, 42·9 % relatedness to A. pushchinoensis and 38·5 % relatedness to A. gonensis. On the basis of the DNA–DNA hybridization data, isolates AB04T and K4T are not related to A. flavithermus DSM 2641T, A. pushchinoensis DSM 12423T or A. gonensis NCIMB 13933T at the species level, but show relatedness to one another of 40·5 %. On the basis of the data presented, it is proposed that strains AB04T (=NCIMB 13972T=NCCB 100050T) and K4T (=NCIMB 13971T=NCCB 100051T) be designated as the type strains of Anoxybacillus ayderensis sp. nov. and Anoxybacillus kestanbolensis sp. nov., respectively.

Recent Applications of High Resolution Electron Microscopy to Crystalline Arrays of Virus Particles

1978 ◽  
Vol 36 (3) ◽  
pp. 470-482 ◽  
Author(s):  
R.W. Horne
Keyword(s):  
Electron Microscopy ◽  
Image Processing ◽  
Analytical Techniques ◽  
Staining Technique ◽  
High Resolution Electron Microscopy ◽  
Optical Diffraction ◽  
Full Potential ◽  
Virus Particles ◽  
Resolution Electron ◽  
Wide Range

The technique of surrounding virus particles with a neutralised electron dense stain was described at the Fourth International Congress on Electron Microscopy, Berlin 1958 (see Home & Brenner, 1960, p. 625). For many years the negative staining technique in one form or another, has been applied to a wide range of biological materials. However, the full potential of the method has only recently been explored following the development and applications of optical diffraction and computer image analytical techniques to electron micrographs (cf. De Hosier & Klug, 1968; Markham 1968; Crowther et al., 1970; Home & Markham, 1973; Klug & Berger, 1974; Crowther & Klug, 1975). These image processing procedures have allowed a more precise and quantitative approach to be made concerning the interpretation, measurement and reconstruction of repeating features in certain biological systems.

Microfabrication research at the National Submicron Facility

1983 ◽  
Vol 41 ◽  
pp. 86-89
Author(s):  
E.D. Wolf
Keyword(s):  
Integrated Circuits ◽  
Particle Physics ◽  
High Speed ◽  
New Technology ◽  
High Energy ◽  
High Energy Particle ◽  
New Science ◽  
Wide Range ◽  
Intermediate Domain ◽  
Circuit Function

Most microelectronics devices and circuits operate faster, consume less power, execute more functions and cost less per circuit function when the feature-sizes internal to the devices and circuits are made smaller. This is part of the stimulus for the Very High-Speed Integrated Circuits (VHSIC) program. There is also a need for smaller, more sensitive sensors in a wide range of disciplines that includes electrochemistry, neurophysiology and ultra-high pressure solid state research. There is often fundamental new science (and sometimes new technology) to be revealed (and used) when a basic parameter such as size is extended to new dimensions, as is evident at the two extremes of smallness and largeness, high energy particle physics and cosmology, respectively. However, there is also a very important intermediate domain of size that spans from the diameter of a small cluster of atoms up to near one micrometer which may also have just as profound effects on society as “big” physics.

Application of TEM to Deformation, Wear, and Fracture of Ceramics

1974 ◽  
Vol 32 ◽  
pp. 472-473
Author(s):  
B. J. Hockey
Keyword(s):  
Wear Resistance ◽  
High Temperature ◽  
Mechanical Behavior ◽  
Brittle Materials ◽  
High Temperature Strength ◽  
Wide Range ◽  
Corrosive Environments ◽  
Further Development

Ceramics, such as Al2O3 and SiC have numerous current and potential uses in applications where high temperature strength, hardness, and wear resistance are required often in corrosive environments. These materials are, however, highly anisotropic and brittle, so that their mechanical behavior is often unpredictable. The further development of these materials will require a better understanding of the basic mechanisms controlling deformation, wear, and fracture.The purpose of this talk is to describe applications of TEM to the study of the deformation, wear, and fracture of Al2O3. Similar studies are currently being conducted on SiC and the techniques involved should be applicable to a wide range of hard, brittle materials.

Observation of Atom Rows in Thorium Pyromellitate Using a Field Emission STEM

1977 ◽  
Vol 35 ◽  
pp. 80-81
Author(s):  
H. Todokoro ◽  
S. Nomura ◽  
T. Komoda
Keyword(s):  
Field Emission ◽  
Amorphous Carbon ◽  
Carbon Film ◽  
Dark Field Image ◽  
Dark Field ◽  
Amorphous Carbon Film ◽  
Atomic Size ◽  
Wide Range ◽  
A Chain

It is interesting to observe polymers at atomic size resolution. Some works have been reported for thorium pyromellitate by using a STEM (1), or a CTEM (2,3). The results showed that this polymer forms a chain in which thorium atoms are arranged. However, the distance between adjacent thorium atoms varies over a wide range (0.4-1.3nm) according to the different authors.The present authors have also observed thorium pyromellitate specimens by means of a field emission STEM, described in reference 4. The specimen was prepared by placing a drop of thorium pyromellitate in 10-3 CH3OH solution onto an amorphous carbon film about 2nm thick. The dark field image is shown in Fig. 1A. Thorium atoms are clearly observed as regular atom rows having a spacing of 0.85nm. This lattice gradually deteriorated by successive observations. The image changed to granular structures, as shown in Fig. 1B, which was taken after four scanning frames.

Development of a conical anode Fe-gun for low voltage SEM

1988 ◽  
Vol 46 ◽  
pp. 978-979
Author(s):  
T. Miyokawa ◽  
S. Norioka ◽  
S. Goto
Keyword(s):  
High Resolution ◽  
Field Emission ◽  
Low Voltage ◽  
Irradiation Damage ◽  
Cold Cathode ◽  
Virtual Source ◽  
Source Position ◽  
Electrostatic Lens ◽  
Electrostatic Lenses ◽  
Wide Range

Field emission SEMs (FE-SEMs) are becoming popular due to their high resolution needs. In the field of semiconductor product, it is demanded to use the low accelerating voltage FE-SEM to avoid the electron irradiation damage and the electron charging up on samples. However the accelerating voltage of usual SEM with FE-gun is limited until 1 kV, which is not enough small for the present demands, because the virtual source goes far from the tip in lower accelerating voltages. This virtual source position depends on the shape of the electrostatic lens. So, we investigated several types of electrostatic lenses to be applicable to the lower accelerating voltage. In the result, it is found a field emission gun with a conical anode is effectively applied for a wide range of low accelerating voltages.A field emission gun usually consists of a field emission tip (cold cathode) and the Butler type electrostatic lens.

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