scholarly journals The conjugative plasmid pSG5 from Streptomyces ghanaensis DSM 2932 differs in its transfer functions from other Streptomyces rolling-circle-type plasmids

Microbiology ◽  
1998 ◽  
Vol 144 (10) ◽  
pp. 2809-2817 ◽  
Author(s):  
R.-M. Maas ◽  
J. GUtz ◽  
W. Wohlleben ◽  
G. Muth
Keyword(s):  
Transfer Functions ◽  
Conjugative Plasmid ◽  
Rolling Circle ◽  
Streptomyces Ghanaensis

scholarly journals Replication of Staphylococcal Multiresistance Plasmids

2000 ◽  
Vol 182 (8) ◽  
pp. 2170-2178 ◽  
Author(s):  
Neville Firth ◽  
Sumalee Apisiridej ◽  
Tracey Berg ◽  
Brendon A. O'Rourke ◽  
Steve Curnock ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Replication Initiation ◽  
Conjugative Plasmid ◽  
Rolling Circle ◽  
Segregational Stability ◽  
Structural And Functional Properties ◽  
Resistance Plasmids ◽  
Genes Encoding

ABSTRACT Based on structural and functional properties, three groups of large staphylococcal multiresistance plasmids have been recognized, viz., the pSK1 family, pSK41-like conjugative plasmids, and β-lactamase–heavy-metal resistance plasmids. Here we describe an analysis of the replication functions of a representative of each of these plasmid groups. The replication initiation genes from theStaphylococcus aureus plasmids pSK1, pSK41, and pI9789::Tn552 were found to be related to each other and to the Staphylococcus xylosus plasmid pSX267 and are also related to rep genes of several plasmids from other gram-positive genera. Nucleotide sequence similarity between pSK1 and pI9789::Tn552 extended beyond theirrep genes, encompassing upstream divergently transcribed genes, orf245 and orf256, respectively. Our analyses revealed that genes encoding proteins related to the deducedorf245 product are variously represented, in several types of organization, on plasmids possessing six seemingly evolutionarily distinct types of replication initiation genes and including both theta-mode and rolling-circle replicons. Construction of minireplicons and subsequent functional analysis demonstrated that orf245is required for the segregational stability of the pSK1 replicon. In contrast, no gene equivalent to orf245 is evident on the conjugative plasmid pSK41, and a minireplicon encoding only the pSK41 rep gene was found to exhibit a segregational stability approaching that of the parent plasmid. Significantly, the results described establish that many of the large multiresistance plasmids that have been identified in clinical staphylococci, which were formerly presumed to be unrelated, actually utilize an evolutionarily related theta-mode replication system.

scholarly journals Functional Analysis of Three Plasmids from Lactobacillus plantarum

2005 ◽  
Vol 71 (3) ◽  
pp. 1223-1230 ◽  
Author(s):  
Richard van Kranenburg ◽  
Natasa Golic ◽  
Roger Bongers ◽  
Rob J. Leer ◽  
Willem M. de Vos ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Bacillus Subtilis ◽  
Host Range ◽  
Lactobacillus Plantarum ◽  
Unknown Function ◽  
Conjugative Plasmid ◽  
Rolling Circle Replication ◽  
Cloning Vectors ◽  
Rolling Circle ◽  
Arsenite Resistance

ABSTRACT Lactobacillus plantarum WCFS1 harbors three plasmids, pWCFS101, pWCFS102, and pWCFS103, with sizes of 1,917, 2,365, and 36,069 bp, respectively. The two smaller plasmids are of unknown function and contain replication genes that are likely to function via the rolling-circle replication mechanism. The host range of the pWCFS101 replicon includes Lactobacillus species and Lactococcus lactis, while that of the pWCFS102 replicon also includes Carnobacterium maltaromaticum and Bacillus subtilis. The larger plasmid is predicted to replicate via the theta-type mechanism. The host range of its replicon seems restricted to L. plantarum. Cloning vectors were constructed based on the replicons of all three plasmids. Plasmid pWCFS103 was demonstrated to be a conjugative plasmid, as it could be transferred to L. plantarum NC8. It confers arsenate and arsenite resistance, which can be used as selective markers.

scholarly journals Complete Nucleotide Sequence of pSK41: Evolution of Staphylococcal Conjugative Multiresistance Plasmids

1998 ◽  
Vol 180 (17) ◽  
pp. 4350-4359 ◽  
Author(s):  
Tracey Berg ◽  
Neville Firth ◽  
Sumalee Apisiridej ◽  
Anusha Hettiaratchi ◽  
Amornrut Leelaporn ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Nucleotide Sequence ◽  
Transfer Functions ◽  
Insertion Site ◽  
Conjugative Plasmid ◽  
Site Specificity ◽  
Significant Group ◽  
Resistance Determinants ◽  
Transposon Insertion ◽  
Clinically Significant

ABSTRACT The 46.4-kb nucleotide sequence of pSK41, a prototypical multiresistance plasmid from Staphylococcus aureus, has been determined, representing the first completely sequenced conjugative plasmid from a gram-positive organism. Analysis of the sequence has enabled the identification of the probable replication, maintenance, and transfer functions of the plasmid and has provided insights into the evolution of a clinically significant group of plasmids. The basis of deletions commonly associated with pSK41 family plasmids has been investigated, as has the observed insertion site specificity of Tn552-like β-lactamase transposons within them. Several of the resistance determinants carried by pSK41-like plasmids were found to be located on up to four smaller cointegrated plasmids. pSK41 and related plasmids appear to represent a consolidation of antimicrobial resistance functions, collected by a preexisting conjugative plasmid via transposon insertion and IS257-mediated cointegrative capture of other plasmids.

scholarly journals Conjugative Type 4 Secretion System of a Novel Large Plasmid from the Chemoautotroph Tetrathiobacter kashmirensis and Construction of Shuttle Vectors for Alcaligenaceae

2009 ◽  
Vol 75 (13) ◽  
pp. 4362-4373 ◽  
Author(s):  
Bomba Dam ◽  
Wriddhiman Ghosh ◽  
Sujoy K. Das Gupta
Keyword(s):  
Transfer Functions ◽  
Protein A ◽  
Conjugative Plasmid ◽  
Secretion Systems ◽  
Gene Encoding ◽  
Host Chromosome ◽  
Shuttle Vectors ◽  
Incp Plasmids ◽  
Damage Repair ◽  
Insertional Inactivation

ABSTRACT Tetrathiobacter spp. and other members of the Alcaligenaceae are metabolically versatile and environmentally significant. A novel, ∼60-kb conjugative plasmid, pBTK445, from the sulfur chemolithoautotroph Tetrathiobacter kashmirensis, was identified and characterized. This plasmid exists at a low copy number of 2 to 3 per host chromosome. The portion of pBTK445 sequenced so far (∼25 kb) harbors genes putatively involved in replication, transfer functions, partition, and UV damage repair. A 1,373-bp region was identified as the minimal replicon. This region contains a repA gene encoding a protein belonging to the RPA (replication protein A) superfamily and an upstream, iteron-based oriV. A contiguous 11-gene cluster homologous to various type 4 secretion systems (T4SSs) was identified. Insertional inactivation demonstrated that this cluster is involved in the conjugative transfer functions of pBTK445, and thus, it was named the tagB (transfer-associated gene homologous to virB) locus. The core and peripheral TagB components show different phylogenetic affinities, suggesting that this system has evolved by assembling components from evolutionarily divergent T4SSs. A virD4 homolog, putatively involved in nucleoprotein transfer, is also present downstream of the tagB locus. Although pBTK445 resembles IncP plasmids in terms of its genomic organization and the presence of an IncP-specific trbM homolog, it also shows several unique features. Unlike that of IncP, the oriT of pBTK445 is located in close proximity to the oriV, and a traL homolog, which is generally present in the TraI locus of IncP, is present in pBTK445 in isolation, upstream of the tagB locus. A significant outcome of this study is the construction of conjugative shuttle vectors for Tetrathiobacter and related members of the Alkaligenaceae.

scholarly journals Initiation and Termination of DNA Transfer during Conjugation of IncI1 Plasmid R64: Roles of Two Sets of Inverted Repeat Sequences within oriT in Termination of R64 Transfer

2000 ◽  
Vol 182 (11) ◽  
pp. 3191-3196 ◽  
Author(s):  
Nobuhisa Furuya ◽  
Teruya Komano
Keyword(s):  
Inverted Repeat ◽  
Dna Transfer ◽  
Conjugative Plasmid ◽  
Bacterial Conjugation ◽  
Binding Ability ◽  
Rolling Circle ◽  
Region Sequence ◽  
Repeat Sequences ◽  
Plasmid R64 ◽  
Termination Process

ABSTRACT Intercellular transfer of plasmid DNA during bacterial conjugation initiates and terminates at a specific origin of transfer,oriT. We have investigated the oriT structure of conjugative plasmid R64 with regard to the initiation and termination of DNA transfer. Using recombinant plasmids containing two tandemly repeated R64 oriT sequences with or without mutations, the subregions required for initiation and termination were determined by examining conjugation-mediated deletion between the repeated oriTs. The oriT subregion required for initiation was found to be identical to the 44-bp oriT core sequence consisting of two units, the conserved nick region sequence and the 17-bp repeat A sequence, that are recognized by R64 relaxosome proteins NikB and NikA, respectively. In contrast, the nick region sequence and two sets of inverted repeat sequences within the 92-bp minimal oriT sequence were required for efficient termination. Mutant repeat A sequences lacking NikA-binding ability were found to be sufficient for termination, suggesting that the inverted repeat structures are involved in the termination process. A duplication of the DNA segment between the repeated oriTs was also found after mobilization of the plasmid carrying initiation-deficient but termination-proficient oriT and initiation-proficient but termination-deficient oriT, suggesting that the 3′ terminus of the transferred strand is elongated by rolling-circle-DNA synthesis.

A simple way for producing holographic filters suitable for image improvement

1978 ◽  
Vol 36 (1) ◽  
pp. 226-227
Author(s):  
K.-H. Herrmann ◽  
E. Reuber ◽  
P. Schiske
Keyword(s):  
Transfer Functions ◽  
Diffraction Order ◽  
Lateral Position ◽  
Simple Method ◽  
Spatial Frequencies ◽  
Resolution Electron ◽  
Wiener Filters ◽  
Image Improvement ◽  
Optical Reconstruction ◽  
Set Up

Aposteriori deblurring of high resolution electron micrographs of weak phase objects can be performed by holographic filters [1,2] which are arranged in the Fourier domain of a light-optical reconstruction set-up. According to the diffraction efficiency and the lateral position of the grating structure, the filters permit adjustment of the amplitudes and phases of the spatial frequencies in the image which is obtained in the first diffraction order.In the case of bright field imaging with axial illumination, the Contrast Transfer Functions (CTF) are oscillating, but real. For different imageforming conditions and several signal-to-noise ratios an extensive set of Wiener-filters should be available. A simple method of producing such filters by only photographic and mechanical means will be described here.A transparent master grating with 6.25 lines/mm and 160 mm diameter was produced by a high precision computer plotter. It is photographed through a rotating mask, plotted by a standard plotter.

Analytic integration of contrast transfer functions

1988 ◽  
Vol 46 ◽  
pp. 822-823
Author(s):  
Peter Rez
Keyword(s):  
Wave Function ◽  
Transfer Function ◽  
Transfer Functions ◽  
Spherical Aberration ◽  
Continuous Distribution ◽  
Objective Lens ◽  
Direction Parallel ◽  
Scattering Angle ◽  
Analytic Integration ◽  
Image Position

In high resolution microscopy the image amplitude is given by the convolution of the specimen exit surface wave function and the microscope objective lens transfer function. This is usually done by multiplying the wave function and the transfer function in reciprocal space and integrating over the effective aperture. For very thin specimens the scattering can be represented by a weak phase object and the amplitude observed in the image plane is1where fe (Θ) is the electron scattering factor, r is a postition variable, Θ a scattering angle and x(Θ) the lens transfer function. x(Θ) is given by2where Cs is the objective lens spherical aberration coefficient, the wavelength, and f the defocus.We shall consider one dimensional scattering that might arise from a cross sectional specimen containing disordered planes of a heavy element stacked in a regular sequence among planes of lighter elements. In a direction parallel to the disordered planes there will be a continuous distribution of scattering angle.

Electron Holography Improving Transmission Electron Microscopy

1990 ◽  
Vol 48 (1) ◽  
pp. 208-209
Author(s):  
Hannes Lichte
Keyword(s):  
Electron Microscopy ◽  
Transfer Functions ◽  
Imaging System ◽  
Spherical Aberration ◽  
Image Plane ◽  
Chromatic Aberration ◽  
Object Wave ◽  
Objective Lens ◽  
Electron Holography ◽  
Wave Aberration

Generally, the electron object wave o(r) is modulated both in amplitude and phase. In the image plane of an ideal imaging system we would expect to find an image wave b(r) that is modulated in exactly the same way, i. e. b(r) =o(r). If, however, there are aberrations, the image wave instead reads as b(r) =o(r) * FT(WTF) i. e. the convolution of the object wave with the Fourier transform of the wave transfer function WTF . Taking into account chromatic aberration, illumination divergence and the wave aberration of the objective lens, one finds WTF(R) = Echrom(R)Ediv(R).exp(iX(R)) . The envelope functions Echrom(R) and Ediv(R) damp the image wave, whereas the effect of the wave aberration X(R) is to disorder amplitude and phase according to real and imaginary part of exp(iX(R)) , as is schematically sketched in fig. 1.Since in ordinary electron microscopy only the amplitude of the image wave can be recorded by the intensity of the image, the wave aberration has to be chosen such that the object component of interest (phase or amplitude) is directed into the image amplitude. Using an aberration free objective lens, for X=0 one sees the object amplitude, for X= π/2 (“Zernike phase contrast”) the object phase. For a real objective lens, however, the wave aberration is given by X(R) = 2π (.25 Csλ3R4 + 0.5ΔzλR2), Cs meaning the coefficient of spherical aberration and Δz defocusing. Consequently, the transfer functions sin X(R) and cos(X(R)) strongly depend on R such that amplitude and phase of the image wave represent only fragments of the object which, fortunately, supplement each other. However, recording only the amplitude gives rise to the fundamental problems, restricting resolution and interpretability of ordinary electron images:

The Effect of Nonlinear Amplitude Growth on the Speech Perception Benefits Provided by a Single-Sided Vocoder

2019 ◽  
Vol 62 (3) ◽  
pp. 745-757 ◽  
Author(s):  
Jessica M. Wess ◽  
Joshua G. W. Bernstein
Keyword(s):  
Transfer Functions ◽  
Spatial Configuration ◽  
Free Field ◽  
Spatial Separation ◽  
Compression And Expansion ◽  
Interaural Difference ◽  
Interaural Differences ◽  
Single Sided Deafness ◽  
Perceptual Separation ◽  
Loudness Growth

PurposeFor listeners with single-sided deafness, a cochlear implant (CI) can improve speech understanding by giving the listener access to the ear with the better target-to-masker ratio (TMR; head shadow) or by providing interaural difference cues to facilitate the perceptual separation of concurrent talkers (squelch). CI simulations presented to listeners with normal hearing examined how these benefits could be affected by interaural differences in loudness growth in a speech-on-speech masking task.MethodExperiment 1 examined a target–masker spatial configuration where the vocoded ear had a poorer TMR than the nonvocoded ear. Experiment 2 examined the reverse configuration. Generic head-related transfer functions simulated free-field listening. Compression or expansion was applied independently to each vocoder channel (power-law exponents: 0.25, 0.5, 1, 1.5, or 2).ResultsCompression reduced the benefit provided by the vocoder ear in both experiments. There was some evidence that expansion increased squelch in Experiment 1 but reduced the benefit in Experiment 2 where the vocoder ear provided a combination of head-shadow and squelch benefits.ConclusionsThe effects of compression and expansion are interpreted in terms of envelope distortion and changes in the vocoded-ear TMR (for head shadow) or changes in perceived target–masker spatial separation (for squelch). The compression parameter is a candidate for clinical optimization to improve single-sided deafness CI outcomes.

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